Most auto parts stores will read the code(s) for you for free.  Any simple handheld OBDII reader will give you the codes.  I have one I got from Autozone for $40.  For more detailed diagnostic help nothing beats Durametric.  It is worth the cost.  I have it and it works perfectly on my 99 C2. http://www.durametric.com/buyus.aspx

With the amount of work it takes to replace the AOS and the engine components removed and reinstalled, and all the other stuff you did, I would start by backtracking over everything you did very carefully.  Like said, 9 times out of 10 this is an air leak.  Did you center and tighten all the plenum clamps? Are you sure you got the intake manifold down tight? Is the throttle body torqued down right and did you use a new seal on it? Are you sure you got the AOS lines snapped in right with new O-rings?  I know by experience this is a very difficult job that requires many steps.  I would start by double checking everything you did.

When my first starter went bad (yes there have been several), go to fire it up and click.  Then second try...click.  Usually it got heat soaked and after waiting 20 minutes or so, it would fire up.  So my best guess is with trying to jump it you have eliminated most everything except the Y-cable and starter.  Are you certain nothing chewed up the wires while it was stored?  The starter solenoid can go bad in a heartbeat.  A brand new Bosch starter has solved my problems for years now.

1) Check that the battery terminals are clean and tight, and the grounding point is clean and dry

2) Check voltage at the battery terminals..should be >12.5 volts

3) Check voltage at the engine bay terminal (where you can jump the car), should be same as at the battery terminals

4) Check and clean the engine ground wire (behind the passenger side wheel...goes from the engine to frame)

5) If voltage is good at the engine bay terminal, take a flashlight and check the wiring to the starter for corrosion or animal chew marks

6) With the clicking noise, it sounds like the starter is not getting enough voltage to kick the starter solenoid

7) You can bypass the clutch switch with a paper clip in order to take that issue temporarily out of the equation

8) Could be that your starter is giving out if all the voltage is correct and the cables are good

9) Could be your Y-cable in the engine bay, known to go bad from corrosion

10) A faulty ignition switch, the electrical part, causes all manner of problems when they decide to let go

11) Try to jump the car at the terminals in the engine bay.  If that works, the problem is more upfront, like the battery or terminals

The car does not need a "reboot" with a battery change.  In fact, exchanging the battery basically does that anyway.  It is not an Immobilizer/Security system issue because you get to the point where the car is sending voltage to the starter to get it to kick over.  It does sound like a low voltage problem.

When you put the key in and turn it to on (not start), what does the voltage read on the dash voltmeter?  It should read just shy of 14V.

Take a look at this part number.  It is a $3.41 new connector.  http://www.autoatlanta.com/tinyresults.php?pn=99965291640;TB_iframe=true&height=550&width=875

You can probably either figure out how the pins come out, or just pry off the gasket and install the new one.

Located here and called a connector housing http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=901-00

http://www.pelicanparts.com/techarticles/Boxster_Tech/102-ELEC-Instrument_Cluster_Bulb_Replacement/102-ELEC-Instrument_Cluster_Bulb_Replacement.htm

Figure 20 maybe...nope...appears different than yours.  However, there is probably another clip on top that needs to be released.  It could be the  two yellow circle items and a small flat blade screwdriver to gently pry on those.  Just guessing....

I would say yes.  Remember, the DME is using the CPS to determine the crankshaft speed and then sets other parameters for engine running.  With an intermittent signal from the CPS, the DME will attempt to set running parameters based on "guess" or default values which are then not optimal for performance.

The engine support bracket has to be loose or it will not align.  See this diagram and make sure you support the engine and loosen all of the nuts, including the engine mount nuts (4, 5, 11). It is a bit difficult, but it can be done. http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=109-00

You can do this, support the engine with a jack, loosen the main motor mount nuts (you probably don't have to remove them all the way), loosen the other engine support bracket bolts and move the bracket around.  I remember having a tough time getting it to align as well, but you can do it.  You just have to have the support bracket loose enough to move around.

The engine bay 12V terminal is right there in the location you pointed out.  It's in a small black plastic box with a big + on it.  Pop it open and make sure the wires have not melted there.  That is the main 12V supply terminal for the starter.

Since you have replaced 7 and 8, then there must be something wrong with the push button switch or a break in the wiring harness.  If you hook up a multimeter to the + wire of the solenoid wiring harness, check to see if when pushing the button you get 12V at the connector.  Also check the wiring harness ground.

Unless it has been relocated, the engine lid emergency release cable is located under the driver's side rear light.  Use a soft plastic wedge and separate the bumper and light and fish around carefully under the light to find the cable.  Like said, once the engine lid is opened, carefully inspect the latch and electrical connectors to the latch to see if anything is loose or not connected properly.

First,  I would not worry about it.  Second, take down the picture of your key.  Copies can be made from a picture.  It would not have the RFID pill to disarm the security system, but some nut case could get access to your car.  Use a ruler or something else.

You should check the evap canister purge valve AND all of the idler pulleys.  Sounds to me more like an idler pulley or maybe the alternator or water pump.

Remember, he is from the UK and probably is referring to idle.  When the ICV goes bad, mostly from being clogged up, the idle wanders, doesn't stay steady and the idle is either to high or to low.  Before you replace the ICV, always a good idea to remove it and clean it with carb cleaner while cycling it with a 9V battery. I soak it overnight and clean it with Q tips. At 139K miles I have had to clean mine several times due to unsteady idle.  Always solves that problem.

Huh.  FWIW I have been using Sears Diehard AGM batteries in my 99 C2 for 10 years.  The first one lasted 5 years, then replaced with equivalent.  I've never had any problems with charging, regulator or alternator problems.  I don't know what difference there may be with a 2004 vs. my 99, but I do not see why a quality AGM battery would not work.  I also run an Optima Red Top AGM battery in my wife's 2007 Mini and again, never had any problems.

99661320600 Trunk Latch Microswitch

From here:http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=803-00

Part No. 9

996 624 118 00

02 03 04 Porsche 911 996 Trunk Lock Latch Actuator Solenoid 99662411800

Earlier models have a mechanical release cable that opens the engine lid.  Later models have an electrical solenoid that unlatches the engine lid.  Not sure if this is the exact one, but many 997 parts fit the 996: http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=997-05-08&section=803-05&pn=99762411800#a

If you look at the part number by clicking on it, it says it is the actuator that controls the spoiler.  However, that being said, it is probably also used by the alarm system to determine whether the engine lid is closed or not when arming the alarm system.  An unlatched engine lid will trigger the alarm system, such as you get when a "zone" is open locking the car...a horn beep.

If you search that part # what you get is the rear spoiler lid actuator.  Is that what you are looking for?

http://www.design911.com/Porsche/996--911--1997-05/996-C2-3-4L-1997-08-01/Boots---Rear-Lid---Locks-and-Latches/pt69_69_1745_-cma81-cmo110-ct345/

Also - http://www.porscheatlantaperimeterparts.com/products/Porsche/2000/911/actuator-THROTTLE-CONTROL-ELE/3793349/99651205500.html

It raises and lowers the spoiler depending on your speed and has no effect on the engine.

I seem to remember this - check your brake lights, all of them including the middle light in the spoiler.  Manually cycle your spoiler up to engage the middle brake light and make sure they all work.  There are also two switches that disengage the cruise control (but do not turn it off which appears to be your problem).  One is the clutch pedal switch  and one is the brake pedal switch.  But I don't think your problem lies there.  You did check Fuse B-7...right?  Anything else strange happening electrically with the car?

There are two switches on the clutch pedal. There is another switch that senses the clutch is not depressed (it is located on top of the clutch pedal) This switch has to be made (clutch in up position) in order to turn the CC on. From my reading, the upper switch must be engaged for the CC to even turn on.  Check the plastic plunger on the upper switch.

Easy enough to check if it is the bulb.  Turn ignition key to the first position where all the lights come on and see if the cruise control light comes on.  Just tried this on my car and it came on for about 2 seconds, and then goes off.

Also be prepared to replace Part 18....the hose connector.  With age and heat those break easily.  You can get a brass hose bib and SS worm clamps from the hardware store that will fit and be done with that problem forever.

I have heard about 2 hours time and $325 at a Porsche dealer for a full four wheel alignment.  Like Loren said, any good alignment shop can do this.  You might check with your PCA chapter to see if anybody recommends a local alignment shop.

The foam is from a flap inside the air control box under the dash or some lining in the vents.  This is a very common problem.  It is a difficult and PITA job to get to the flap, and you cannot just order a new flap.  What most have done is vacuum up the mess, keep a pair of tweezers in the car and pull the stuff that gets stuck behind the vents, and wait patiently until all the bits and pieces stop coming out.  That will happen.  Mine did this a few years ago and it was definitely annoying.  But after research decided to wait it out.  Funny thing is, I've never noticed any difference in the air flow/direction to the various outlets since.  Seems to work just fine without whatever that foam on the flap is for, or the vent work linings.  Actually has been a long time since anymore came out, so I figure problem resolved.

BTW, there is a pollen filter located just where you said, to the left of the battery.  Should be periodically replaced. Doubt that is the source of your problem unless it is old and very deteriorated.