flash it back to stock and see if fuel trims correct themselves, if they do then it is the tune itself. If not, check for any vacuum leaks around intake.
Check for vacuum leaks around brake booster and the hose going to the intake manifold. Next i'd check for leaks from intake piping and intercooler pipping.
Glad it's running strong!!! Yeah like I said before 9/10 UCD tech don't check cars for tunes, especially these. My previous dealer had a couple from CarMax come in because they couldn't pass state inspection due to tuned pcm's. Of course I kept them after replacement lol. I had 3 spare SI pcm's...
Bought as certified Honda or from random used car lot? 9/10 used car techs don't check these cars to see if they're tuned. When I worked for my dealer as UCD tech, I had a couple Si's traded in that were tuned and needed PCM replacements because customer's did not bother tuning back to stock...
From what I've read on the first post, it sounds like you had a bad coil. Pretty common on turbocharged engines. I've seen it happen from old 240's with sr20's to modern day cars like the turbo ecotecs Chevy puts out. The heat eventually messes with the coil. Everything will be fine under vacuum...
Best way is to have a scanner and monitor cylinder misfires while driving. Have someone watch the misfire counter on each cylinder while you're driving under boost or WOT to duplicate the issue. When it happens you'll see which cylinder is causing the issue under boost.
LOL at them saying the bumper needs to come off.....bish please, all you have to do is either remove the fog light garnish or if you have the car in the air, pop out 3 black clips and take out the 10mm bolt to move the splash guard. Stick you hand in and change out the bulb. Literally takes 5...
My ID goes way back to the days of AIM lol I'm dominican, cuban, and puerto rican....so i was trying to think of a screen name at the time and said well hell just put it all together...and BAM Domicubarican was born hahaha. STILL rocking it since 2002 lol
This is actually not brake hold, it is called Hill Assist. 99% similar to brake hold but only used when on inclines. Helps the average driver not roll backwards during stop and go driving on inclines. Only lasts for 2-3 seconds before it disengages and you do in fact start rolling back.
Brake...
No, they are not required to drain the trans before replacing the shaft. You can request them to do a trans service with the shaft replacement but it really isn't necessary to do the job.