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While the cylinders may be scored, I doubt bore scoring will trip the very specific intake valve lifter codes. It sucks that one cannot inspect the lifters without removing the cam cover, which involves a lot of labor. That's why the factory manual recommends replacing ALL the lifters (intake and exhaust) of the bank that is affected. The logic is if one lifter went bad, it's possible the others could follow since they wear similarly and are subject to the same operating conditions. If the mileage is high, it will also be a good opportunity to replace the timing chain pads.
Great numbers. Spec is 0 degree +/- 6 degrees so yours are way within spec. You may want to read or re-read the two threads I mentioned before. They have identical symptoms and intake valve failure.
Excellent. I'm not too familiar with those codes but per the DME 7.8 diagnostic info for 996 P1362 is intake valve of cylinder #4 does NOT switch to small lift i.e. stuck at large lift. That makes sense because at low rev, the intake valves should use small lift and they change to large lift at higher rev. That's how variocam+ works. You mentioned misfires occur only at low rpm. That's because the lifter #4 is stuck at high lift. P1371 is a general lifter code for any cyl #1-#6 do not switch to small lift. I think it's time to remove the bank 2 cam cover and inspect all the intake valves. BTW, can you check the "Cam deviation" readings of both banks? Are they solid and remain constant regardless of revs? This does not change the above but I am just curious about the general health of the engine.
I would recommend doing the e-gas recalibration first, then verify fuel pressure. Note it's normal the fuel pump only turns on for about 1 second to prime the system at cranking. The fuel pump will keep running only if the engine fires up. That's a trivial safety feature.
Check out this thread. Not saying this is your problem but definitely a possibility. https://rennlist.com/forums/996-forum/861911-stuck-lifter-symptoms-misfire-on-cylinder-4-intermittent.html
In the meantime you may also want to attach a vacuum gauge at the intake vacuum to see if the needle are bouncing. That will tell you something mechanical is bad such as a burnt valve, broken valve spring, bad lifter, etc.
What year is your 996? You may need to check the injector and coil signal with a scope. If those are normal, then it's likely a mechanical issue such as a bad lifter.
What are the cam deviations, FRA and RKAT on each bank? Just a sanity check...
Have you performed any compression and leak down tests? What are the exact error codes?
A healthy reading should be less than 1 / second square at idle (after fully warmed up). Have you tried replacing your sparks plugs and coils? You can swap the coil with another cylinder and see if the misfire follows the coil. Did you just get the car with this problem or the problem just developed recently.
In that case, why not get a Durametric first and if it's truly a -19 degrees cam deviation, you can consider redoing it again by yourself as long as you have the proper special tools. If not, you can use it to further diagnose your problems. You can read the misfires of individual cylinders in real-time. Your bank2 variocam would have been diagnosed much quicker if you had Durametric. You can also use the Durametric to verify the timing is done properly. Also, when you don't need it anymore, you can sell it and get back at least 50% (2 free VIN slots out of 3) of what you paid.
Either will be able to re-time bank 1 but before any work the cam deviation should be read to confirm that is indeed the proble first. Did you mention an indy replaced the bank 1 variocam pads? If so, they should redo it under warranty.