Installed the new PTU today and it didn't fix the missing problem.
However, the stuttering (when revving gradually in neutral) _seems_ to have improved, but I'll give it some time before I jump to any conclusions.
As far as my crazy ISC is concerned it seems to have a mind of its own. Today I was testing the ISC and I noticed that when I turn the AC on the counts go down and when I turn it off they go up. This is completely opposite of how it should be and this is a different result than what I had found before. WTF? I swear this car is possessed.