Could be anything, starting from a dodgy connection to something more mechanical.

start ruling out the electrics proceeding per grades:
- check the battery connections, to and from, clean them from oxyde and fit them with a little grease (I had a "sneeze" on my 907 and was the battery POSITIVE Oxydized!!!!!)
- check all connectors for play and oxidation, refit with connectors grease
- check ALL grounds take them out, clean, put them back with connectors grease
- check the KEY SWITH , they get loose and with the vibration they start to heat up and create circuits breaks.
- check the EMERGENCY STOP SWITCH , The loom tends to short where it meets the switch
- do you have the DIGIPLEX or the Modules? you have to borrow separate sets from someone and check if the problem is there.


Mechanical...
have you checked compression? maybe one valve is burned and there you have the back fire and the sputter.

FUEL
The carbs must be synched properly, only with a meter you will see that; They are chap or you can make your own meter using two plastic bottles and some clear pipe.

Plugs
replace them, years ago I got crazy with an old BMW I was restoring, everything was new and properly set and still it would backfire and eventually one cilinder would die, I then fond out that for some reason one of the spark plugs (new out of the box) was the culprit.

I've merged your posts so it`s easier to follow (what was already done or suggested)

you can't do it with out some sort of air flow measuring device, you can make your own fairly cheap or buy one for around 50usd They are simple devices easy to make and details can be found in the FAQ

I have some pilot jets showing up tomorrow.. still running the 40's... Got 37.5 and 35.. I have checked all but the ignition and kill switches, I will investigate those...

New battery and 37.5's definitely helped, no more backfires through carb... Last step is syncing

:update:
bike running great, still has just a slight stumble when you just crack the throttle, but running pretty much perfect otherwise.
140 main, 37.5 pilot, needle on third clip(dyno jet) and 3.5 turns out on mix screws..

already sick of it ?
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