DBJoe996

First try using the jumper at the fuse block with a good 12V battery, not a charger or battery maintainer.  That will not provide enough amps to trip the hood release.

Second, do not pry on the headlight, that is not the proper procedure.  Get a rubber type of wedge and make a space between the rear bumper and left rear tail light.  Fish around under the tail light and find the emergency release cable for the engine lid.  Pull it and the engine lid will open.  Then use the jumper points in the engine bay with a 12V battery to power up the car.  The hood release should then work.

Finally, once you get the trunk open, do yourself a big favor and pull the passenger headlight, locate the trunk emergency release cable and re-route it to just behind the front bumper tow hook plug.  Next time the battery goes dead, simple enough to pop the tow hook plug and pull the release cable.

Describe water damage.  Did any of the relay or fuse panels get wet?  I assume that you have pulled and checked every fuse.  What about the main power distribution box located on the firewall in the passenger footwell?  There are 80 amp fusible links in there that if they got wet (or corroded) might not function correctly.  Does Durametric return any  error codes?  Have you checked for spark?   Yes, it is true if the CPS is good the tach needle will bounce when cranking the engine over.

One other thought - when you switch on the AC, do both radiator fans come on low or are they delayed as well?  And when the AC does finally start working, are both left/right radiator fans coming on?

There is also an AC compressor relay in Relay Support 2.  Might think about replacing that relay to eliminate a potential problem.

I don't know of anyway to actually test them other than does the ambient air temperature read correctly on cluster?  The HVAC system uses the temperature differential readings between the outside air and cabin air when you use AUTO setting on the HVAC control panel.  The system then cycles on/off the AC compressor as needed for the desired cabin temperature.  The way to get around that is to manually set the fan controls/temp.  The second thing that I have heard/read about is a sticking or faulty pressure switch causing delayed AC.  Part #21 here  http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=813-25

Is your ambient air sensor located correctly in the front bumper?  Also, there is a interior temp air sensor located behind the little plug on the passenger side on the dash.  I would check that too.

How about pulling the scavenger pump on Bank 2 and checking it?  Seems like if the e-clip got stuck in there, the scavenger pump might be messed up?  Simply a thought.....

Get a bigger hammer!  What I mean is you may have to try to rotate it by banging on it with a hammer to unfreeze it.  It is plastic in a metal hole, so eventually it will move.

I would say the simple answer to your question is no.  I think you might have to backtrack and make sure all of the wiring is connected right, including the DME.  Might help to unplug the DME connectors and plug them back in again.  Do the power functions of the seats work?  After that, do a complete system reset by removing the negative battery lead, wait 15 minutes, reconnect and see how things work.  If after that the problem is not resolved, you might have to start checking fuses and relays.

You also need to check the vacuum lines.  See this forum thread https://www.6speedonline.com/forums/996/208326-code-p1516-intake-manifold-switchover.html

Also, if you have a MAF sensor, clean it with MAF sensor cleaner.  It has been known to cause ABS/PSM faults and rough idle.

Hate to say it but it seems something is wrong with the HVAC control panel.  If I push the snowflake button, that engages the AC compressor to pump freon through the system, and I can manually put the fan speed anywhere from low to high, and direct the air manually to defrost vents, dashboard vents and floor vents, any or all of these.  To put the system in maximum cooling mode, hit the snowflake, put the temp control on LO, push the recirc button, push the dashboard vents button, and manually put the fan on HI.  As far as I know, when in this mode (or for that matter any other mode other than AUTO), the fan speed is independent of the AC mode and operates anywhere from LO to HI.

So it comes back down to...why when you engage the AC does the fan blower not manually operate from LO to HI?  It should.  So I think something is wrong with your HVAC control panel.  Another question, what does your voltage read when you engage the AC?  Does it drop a lot or stay fairly steady at around 13V?

Record your mileage before sending it in for repair.  Mileage is stored in the instrument cluster.  Good luck on the repair.

Stupid question - are you running it in the Auto mode or manual mode?  In other words, what happens if you switch the AC on and use the FAN button to increase the airflow?

Actually I don't know where #35 can be seen or reached.  Sorry not much help there.  May have to trace the steering shaft up under the dash and go from there.  Someone else was having some problems with new Conti tires.  Seems molding lubricant in tire manufacturing was making the tires feel slippery.  Have you considered a Hunter Road Force balance?  Could be something going on with the tires and wheel combinations.  Are you running wheel spacers?

Seems you have replaced just about every part that would play a role in this, and had things checked and an alignment done.  Not that it is common, but I wonder if the steering shaft has some play in it, i.e., the spline shaft and the universal joints.  Might be worth it to check the bolts that hold the steering shaft #10 and #35 here - http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=403-05

Bleeding the clutch system might help, but if the deterioration has been over some time and simply now is worse, my guess would be the clutch master cylinder seals and not the slave cylinder.

There is a rubber stop Part #9 here http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=801-40

Check the obvious to begin with...fuses and relays.  With a multimeter, see if the latch actuator is getting power when the button  is pushed.  Could be the button, but more likely the latch actuator.

You can find the drive motors and microswitch (which usually is the culprit) here: http://www.autoatlanta.com/porsche-parts/hardparts.php?dir=996-99-05&section=811-01

Maybe this will help, and a 2 ton bearing puller

https://rennlist.com/forums/964-forum/663697-c4-front-inner-cv-boot-or-joint-repair-2.html

I would pull both of the overhead infrared sensors and check them out.  Could be one of them is shorted out or bad.  Check the wiring as well.  See if there is a short to ground.

vacuum lines.pdf

Post here 

First off, drain all of the coolant and flush the system with water and Dawn liquid soap.  All the coolant hoses will deteriorate rapidly with oil in them, and replacing all the coolant hoses is a massively expensive job.  Second, why not try to determine the intermix problem?  Could be a bad AOS or oil cooler O-ring problem, not necessarily a total disaster.  You say you are in too deep to attempt to fix, but you are willing to buy a good used engine and do an engine swap?  I think maybe you should  consider talking to a knowledgeable Porsche mechanic or Indy about the intermix problem, establish a plan for why that is, perform some checks and tests, and then determine if the engine has failed (d-chunked) or just some component that has failed.

Good technical article on 986 Boxster AOS replacement - https://www.pelicanparts.com/techarticles/Boxster_Tech/09-ENGINE-Air_Oil_Separator/09-ENGINE-Air_Oil_Separator.htm

My go to site for finding  parts and part numbers  http://www.autoatlanta.com/porsche-parts/911.php