If you're not using any kind of source control I'd suspect it'd be absolute chaos organizing it with multiple coders.
I split time on 3.5 rc4 and 6. My only issue there were some issues with other monitors while testing in fullscreen. A regression from 3.4 perhaps, I've never encountered that before so who knows. The only alpha I've used was like alpha 5 or 6 so quite a ways before whatever we are on now. Beta is coming soon though so hopefully whatever crashes yall are getting on an engine level gets cleaned up by that.
Is the 3D pipeline much different from 3.4? I have a pretty massive code base to move over once 4.0 hits stable and I kinda dread it lol.
Even if you got HTML5, I suspect performance would be vastly superior with a binary as opposed to the browser. The stutters you guys reported getting at the beginning of the game sound like the uber shader stuff compiling but that is just a guess.