Well, it's the plan I would take. Have no fear, your bike did not get damaged by running it without any O2 sensors. It's just that I don't see what it would really prove because you would be injecting other problems into the mix to some degree...
The more I read and re-read your thread it almost seems like the "hit bump and engine miss" problem only happens when the T-max is installed.
It's a shame you have to buy a new pair of narrow band O2 sensors just to restore the bike back to stock status for testing. But this time after using them, put them in a safe place!!
My approach would be to install the original factory ECM (I assume it is the original factory unit that came with the bike) & install the narrow band sensors. Perform a WOW test. I would expect to see at least a P0154 & P0134 coded logged to the ECM when it was used by the dealership without any O2 sensors hooked up. Record any DTC codes (just for the record) and clear the error log for all devices (TSM, Speedo, ECM) on the communication buss. Be sure you see the word "NONE" for each device. NoRsp (no response) for any device the firmware supports but is not present. You must see the word "NONE" for devices that can be seen by the speedo on the buss.
Install the low flow air cleaner. Ride the bike and note any & all performance issues. Assuming the original ECM is good (and at this point I feel it is good), my guess is the bike may have de-acceleration popping, but it should not have an ignition buck or acceleration drop out etc.
While you ride, keep an eye on the check engine light for indications that you have trapped a DTC. Especially under hard acceleration, take a peek for any indication of a check engine light.
Ride the bike over some bumps. See if the symptoms have changed vs the T-Max.
The "capture rate" for errors that these ECM's have is fairly slow. I don't believe the built in WOW tests are ran in "enhanced" mode so an error that happens has to last fairly long for the ECM to log it as an error. Therefore a self healing error that happens only for a couple of milliseconds (say for example the crank sensor pickup misses 1 small window flag in 100 revolutions) can and will be felt by the rider but it may be outside the "failure window" to be captured & logged as an error by the ECM. If you find a particular driving habit that shows a performance anomaly, repeat it several times to try and force a code to log.
You have to fix the "hard engine miss under acceleration" & "engine misses while riding over a bump" first. Under WOT, the fuel map goes open loop and you should have plenty of fuel to make a strong pull. It may be a bit lean but you should not experience any bucking,,hard electrical engine misfire or exhaust "backfiring". It may feel like the engine is running out of steam (lean condition) but it should still be a "smooth weak pull". De-acceleration popping, plug readings, weak engine strength are all secondary right now. The problem you have with "riding over a bump & the engine misses" must be fixed 1st.
See how much information you can collect.
BTW,,I am not good with features vs bike models. Is your ignition switch mounted on top of your gas tank or is it at the steering neck like on my FXDL. Also are you working with a factory manual & schematics for a 2007 FXDB.
