Hondata

I have a 2011 Si Sedan(Want ALL Motor ONLY) with
Injen CAI
Skunk2 Alpha Race Header
Skunk2 76mm Mega RR Exhaust
Hondata FlashPro

Im using the Base map of CAI Skunk2 header and catback tune. And the car bogs out sometimes and just isnt running like it did when I had only the Injen CAI tune but i didnt have the header installed yet. Now my questions r
1. Is the exhaust too big to run that tune?
2. Secondary 02 sensor has issue but I have read that people r disabling them, Is that gonna make the car run weird?
3. I have the primary skunk2 02 sensor extender on the front and a cel eliminator on the secondary 02 sensor spot, is that right and if I disable the secondary 02 sensor in flashpro can I just leave it there
4. Something sounds weird but when I looked under the car everything was tight and looked good, I read some people said that the exhaust hits the subframe when u add the race header(I didnt c any spot it would hit)
5. I'm gonna get a ProTune but want to get Skunk2 Throttle Body and Intake Manifold but I go to the track so I might just do it now cause I have Skunk2 springs and Sport Shocks on the way and I wanna make it to the track

Any help would really B appreciated

I data-logged 3 little runs and disabled the 02 but check engine light still went back on and do I have to unplug battery to get service light off?

Very good questions here:

1. No, K-motors LOVE big exhausts like the S2 76mm
2. No, disabling it will have no negative effect on the car but if you want to get it tuned by a professional I would ask him how he wants it.
3. The O2 extender on the front will cause you issues, the primary O2 sensor needs direct exhaust readings to properly trim engine fuel, you will have to remove the primary O2 sensor and cut and extend the wires about 5 inches for a good fit. You truly dont need the secondary sensor but like I said ask your tuner.
4. The header will hit the steering rack if you do not have solid motor mounts. Also the cat-back exhaust system might be hitting in the back either on the spring or the frame piece under the bumber with the hangers.

I have already gone through your exact same troubles so I know how frustrating it can be. The car may be bogging due to the O2 sensor issue which is why your CEL is on or you could try switching from MAP to MAF or from MAF to MAP on you flashpro and see if that makes everything better but I would only try that after you fix your O2 sensor issue because that will throw everything off if it is not reading properly