I have the same Oem exhaust mod.(replaced the 2 big perforated pipes)
I have not this pop sound !
I think your problem is caused by your secondary cats. removal ,your car sound's also match more raspy than mine.
So...when it's possible,mount your secondary cats. back on(with clamps) ,and give it a try.
BTW...when i step on it during cold start cycle sometimes i hear also a bit backfire .
Conclusion....i think nothing is wrong here,and when you want to be sure,mount your secondary cats. back on,and when it still pops (backfires) than there is another problem...running to rich,and that you must see on your fuel consumption.