A quick update since it's been so long.
Over the past 2 months I've been running the stock intake with APR's 93 oct program and water meth off.
I still get misfires, and have logged them extensively for APR's support. I've re-created every situation I misfire in, including a few 4th gear pulls where i expereienced several pops when passing through 5,500rpm. FYI - The misfires ARE showing up in all my logs.
Requested vs. Actual... everything... looks good. Fuel trims, boost pressure, rail pressure...
So I can appreciate APR having trouble tracking this down as the car logs show the engine is working as expected. I am however, dissapointed with the lack of support from APR throughout this.
I've returned logs whenever requested - usually within a few hours of being asked. I have gone through every conceivable piece of hardware on the vehicle and tested/replaced everything that could be causing this.... I've spent thousands and thousands of dollars chasing this problem down over the last year as has been documented in this thread.
I have purchased every APR product they make for my car, and I still have yet to have any useful help from them on this issue. I am extremely frustrated and I cannot imagine how this is not a software issue at this point and thus I am moving on to try another tuner.
Now for the good news - Both Unitronic and GIAC have stepped up and offered to give me a 30 day trial of their software! I am going to trial the GIAC software first, as they have a 100 oct tune. I'm also excited that they will give me a tune to take full advantage of all the upgrades I have on my car. I've scheduled track time on May 16th and will be logging my runs.
I will post up my results with the new tune as soon as I can.