S4R Misfiring/Running warm/Loud backfire

Hello,

I have an S4R with a KN filter (no holes in box) and akropavich (Sp?) exhaust.

I recently REMOVED a power commander, and a mid pipe that was a straight pipe replacing the udder.

On a ride last night, I noticed that the bike would missfire(?) at low rpms, usually when taking off, almost causing a stall, along with the bike running hotter than normal (50F day, typically have trouble keeping the engine warm enough to idle, and when I got off the freeway it was almost 200F) as well as random, extremely loud back firing when engine braking.

I originally purchased the bike without these mods, and the bike didn't give me trouble. Installed these mods, still no trouble. Now that I removed them, I have issues.

I've googled a bit and it appear the back firing may be the exhaust gaskets leaking, so I will look at them when I work on the bike. I am curious however, since when I was taking the power commander off I was also distracted by my 2 year old step daughter, if I may have accidently SWITCHED the injectors on the cylinders. Is there a sure fire way to check to make sure they are on the correct cylinders?

Thank you in advance.
Mike