DBJoe996

The best maintenance to do is change your oil/filter frequently, i.e., <5,000 miles.  Also get the LN Engineering spin-on oil filter adapter and LN Engineering magnetic drain plug.  http://lnengineering.com/

Yes, I agree with this as well.  I wonder if the OP has the means to do this.  From our perspective, we know it would be the wisest choice to NOT start the engine and check out what has been said, everything from oil filter inspection to pulling the plugs, checking the pulleys and slowly turning over the engine by hand.  He will need to determine what is going on with the engine first, and that means getting in there to inspect, check and go over things.  If he does not have the capability or knowledge to do that, he needs to get his car to a reputable shop for diagnosis.  In the end, it's a rather expensive gamble to keep trying to start it without knowing exactly what is wrong.

And JFP and Ahsai, I know your knowledge and reputation well, and I have much respect for your wisdom in dealing with these cars and engines.  I only hope  the OP listens.

I'm with Loren on this one.  You said spark plugs inspected w/29K miles on them, but you didn't say you replaced them.  Point in case, recent misfire on my car.  Determined to be bad plugs, and I only had  24K miles on them.  Replaced with new plugs and no more misfires.  Put in new plugs.

2 hours ago, JFP in PA said:

 

That is not quite correct.  A battery alone should show between 12-13 V; it would only show 14V with the engine running, assuming the alternator is working correctly.

Well I do agree.  It is approximate just going by the dash voltmeter.  The best way would be to put a multimeter on the battery and determine the true voltage, or do a load test on the battery. But my point was it should be higher than what he said it shows.  And then goes straight to zero when he tries to start it.  Something is causing a huge voltage drop, or the battery has no capacity.

First, 12V then goes to 0V when you try to start it is not right.  12V is not enough to spin the starter, so your battery is not charged.  Should be closer to showing 14V on the dash voltmeter when the ignition key is turned on.  That it goes to 0V is strange, like the battery has no reserve capacity and is just dead.  Maybe your new battery has a bad cell and cannot hold a charge, or a busted cell internally.  Happens.  You are going to have to first figure out what is going on with the battery.  Maybe swap one in from another car, or have the local auto store test it.  You could also try jumping it to see if it will start and stay running.  Have you had any problems with the alternator or voltage regulator?

I assume since you are getting an OBDII reader, the CEL is on?  Good to find out what codes it shows.

When you push started it, how did the engine run?  Rough?  Normal?  Did the dash voltmeter show more than 12V?  One thing I'm thinking is the battery is bad with low voltage, maybe internally shorted, and the car simply cannot run for very long with the electrical system draw while running (think fuel pump running, coils firing, etc.)

The grinding noise I'm not sure about, but these engines make some strange sounds when they are not happy.  The popping noises could be caused by the low voltage, i.e., the coil packs not getting enough voltage to fire, so they fire intermittently until the whole thing just dies.

Sorry, not enough to go on.  So the engine died.  Was the "popping sound" exhaust or mechanical? Does it crank but not start?  Is the CEL on?  Do you have an OBDII reader and can check for codes?  Type of car, year, recent maintenance or repairs?  What does the voltage read when you turn the car on but don't start it?

One reason you may not be getting any advice is that no one can understand what the problem is.   What do you mean?  The "clutch pedal extended further than it had been previously" is not clear.  Please explain the problem in more detail.

I think your thinking is right, they got water in the alternator and it fried the voltage regulator, then that in turn fried your HVAC display.  Hopefully, a replacement will end your saga.

Try resetting the memory for seat/mirrors.  With key in ignition and switched on (both doors closed), set the desired positions for seat and mirrors. Keep memory button M depressed and press either 1, 2, or 3.  Turn ignition off and remove key.  Then try it while locking/unlocking car.  I know on some modern cars the seat/mirrors positions are saved along with the key fob, but I'm not sure that is the case with our 996's, at least not my 99 key fob.

The manual also states that when pushing the memory button, the lumbar support and mirrors positions will be completed even if the memory button is not kept depressed.  I have heard that sometimes the electrical contacts in the memory button panel get gummed up, and removal, cleaning the contacts and testing clears things up.

Agreed that seems unacceptable, but probably something you should have asked about first.  Did they install a new clutch fork and release bearing?  I believe there is an updated version Unfortunately to replace the transmission has to be dropped again.

http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=301-00

For 2. - #6 and #8 perhaps on the bolts...not sure what you are missing

http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=605-00

I agree with Loren.  Do those things first.  I will assume that the car did not exhibit this behavior prior to replacing the alternator, so the first rule of mechanics is to go back to the last thing you did.  I know it will be a pain to pull the alternator once again and have it tested but that is what you need to do.  Also, it is possible to get a bad one out of the box.  I see you say "new" alternator...was it brand new or reman?  If it were me, I'd pull the alternator and take it back to where you bought it and get another new one.

I think this may help because it shows how far you have to get in there to replace the cruise control bulb

http://www.renntech.org/forums/topic/49303-2003-porsche-996-instrument-cluster-bulbs/

And this might help a little to: http://www.pelicanparts.com/techarticles/Boxster_Tech/102-ELEC-Instrument_Cluster_Bulb_Replacement/102-ELEC-Instrument_Cluster_Bulb_Replacement.htm

And this: http://www.boxa.net/forum/index.php?/topic/59708-how-to-replace-instrument-cluster-lights/

Have you checked the tire for road debris?  I know that is really simple, but I have had rocks stuck in the tread that makes the same noise.  Also picked up a large bolt one time.  Stuck straight in and I could actually feel it when rolling.  Ruined the tire.

I agree with Ahsai.  You need to start with checking for a vacuum leak, particularly on the intake side of things.  Too much air getting sucked in will throw off the MAF and cause lean running.  Also, having cleaned the MAF many times, I finally replaced it with a new Bosch MAF and that took care of that.  Very carefully inspect your oil filler pipe as they are prone to cracking and that will cause a vacuum leak.  Might just replace that as well.  By process of elimination given that many various codes you will have to go step by step.  Also, buy your own OBDII reader.  They are cheap and valuable.  Better yet, get Durametric for troubleshooting.

Either the window is not tight against the window seal, or the door membrane behind the door panel is not sealed.  See this article for door disassembly http://www.pelicanparts.com/techarticles/Porsche-996-997-Carrera/76-BODY-Door_Panel_Removal/76-BODY-Door_Panel_Removal.htm

You could disassemble the door and have someone gently spray water from a garden hose around the window to see if you can locate the leak.

I think Ahsai is pointing you in the right direction.  I know throwing money at a problem is difficult but more than likely what you will need to do.  Get the correct 02 sensors.  I cleaned my MAF sensor multiple times to no avail - so I replaced it with a new one and my problem was solved.  Remove the throttle body, then disassemble it.  Clean it completely with TB cleaner.  Clean out the Idle Control Valve because it really gets gummed up.  Make sure it is working smoothly.  I have found removing the TB and cleaning it is really the best way to ensure it is totally cleaned out.

AOS is what comes to mind....there is a diaphragm in there separating the coolant from the crankcase side.  If the diaphragm leaks or is totally blown, or the AOS cracks internally, coolant has direct access to the crankcase. Since the crankcase is under vacuum and the coolant is under pressure, it would rapidly dump coolant into the crankcase.  Worth a check.  Sound like you have checked everything else.  Hope it works out!

What happens if you use the key to lock/unlock the door?  The reason for asking is to determine if there is a difference between using the remote and using the key.  If the key creates the same situation, passenger door not unlocking, then I believe the only solution is a visit to a Porsche dealer for reprogramming the security module in the car.  Given that the battery was disconnected for some period of time, the security module probably went into "default mode".  I've heard others complain about this same situation, i.e., when unlocking the car only the drivers door unlocks and to open the passenger door one must use the dash lock/unlock button.  It is something that can be programmed (I believe) only with the Porsche software at a dealer.  If for some reason there is another problem with the passenger door, microswitch or locking mechanism, they can also pinpoint that problem as well.

To the best of my knowledge all modern cars use the double pull unlocking from inside.  In other words, when the door is locked just pull on the interior handle twice to unlock and open the door.

Also found this helpful Pelican Parts technical article on P0455 problems and resolutions:  http://www.pelicanparts.com/techarticles/Porsche-996-997-Carrera/106-FUEL-Replacing_Your_Fuel_Line_Vent_Valve/106-FUEL-Replacing_Your_Fuel_Line_Vent_Valve.htm

http://www.renntech.org/forums/topic/10045-cel-code-is-p0455/

It might be that the vacuum leak is significant enough to lean the start mixture to the point you get a no start condition.  A very good diagram of the evap system is in the link.  Seems you are going to have to check everything from a crack in the evap canister to a loose fitting somewhere or one of the valves not working properly. 

If it went all of a sudden more than likely it is the small plastic fitting on the coolant line that runs from the coolant pump to the AOS.  It is right in the center just to the right of the alternator and the oil filler tube.  I hope it is something simple like that.  It is best to repair that with a brass hose connector and some SS clamps.  Other than that everybody else has mentioned all the problem areas: water pump, coolant tank, coolant tank cap.

Agree...driving it hard when the engine is telling you something is wrong is not going to fix a problem!  Since you have access to someone with PIWIS, you need to actuate the bank one VarioCam solenoid and test it, and monitor the cam sensor.  Agree with JFP, either a cam sensor, actuator or VarioCam unit itself.  Also, since you said you don't even know what oil is in it, do yourself a favor and change the oil/filter so you do know exactly what is in it.  Your taking a $15-$20k risk (replacement engine) and I don't understand why you would do that....but hey, it's your car and your money.

Check all your drains.  Sunroof drains are notorious for getting blocked and making the rear carpet wet.  Do a search for drains and then check them all.

http://www.renntech.org/forums/topic/7791-cautionary-warning-heads-up-for-cab-owners/#entry69808