I just wanted to add my 2 cents here and share my experience. Not sure on your mileage, but my '16 is at 43k. I've been running BM3 s2 for a few months. I upgraded my charge pipe as well right before flashing. Like you, I experienced driveability issues that were not present when I just had the JB4. I also have a catless downpipe, afe intake, and modded m2 exhaust(which were all present before flashing). I thought for sure I had a boost leak after installing charge pipe and flashing. Turns out I maybe had a combination of things going on. I will list some thoughts and issues I dealt with:
If you haven't already, make sure you switch your spark plugs out from stock. I did mine a few thousand miles before flash tune.. some say OEM are fine, others recommend one step colder plugs. I ended up using NGK97506 after reading a bit. Make sure they are gapped correctly ... also a bit of conflicting data on this. I started out with a gap around 0.018 and now have them set to 0.024
Make sure you check those o-rings on the charge pipe. Not so much the throttle body side, but the FMIC side. This was a PITA for me.. especially being xdrive. I switched this thing 3 times because it probably wasn't seated right. Make sure the lip of the o-ring can mate with the FMIC.
If you have meth bungs on the charge pipe make shre they're tight and use some teflon or thread locker. They often come loose from the factory.
Not sure which brand of charge pipe you have, but make sure the clamps are tight on where the sleeve would connect the 2 pieces (if it applies to you).
If you're on stock ignition coils, at least one may be acting up. I only came across this as I started to have cold start issues with some lumpy idling and fumbling during starts. I replaced the coil on cylinder #2 and that cleared up almost ALL my driveability issues. Turns out perhaps the o-ring on the charge pipe may have been incorrectly seated as well. But, it was likely a coil starting to act up that was causing the majority of my issues
The car pulls like freight train now and my timing is on point. One thing to note...you need to replace FMIC.. mine is stock now as well and IATs can climb over 40 degrees just doing a few spirited runs. I have one on order now. Not only can the heat rob your power, but it's probably not good to continuously run the motor like that. Also, there's a lot of other factors that may contribute to overall boost/timing. Maybe try switching which fuel station you use if you happen to use the same one.. or add some boostane if the timing is weird to try and rule out fuel as a cause. Techron may help clean some things up as well.
Ok that's about all I got for now.. best of luck.
