**Problem Solved (or never existed)**

So I just put my motor back together, and while I was pretty sure I got the cam lined up correctly, (using the little horizontal notches on the end)  and the piston right at TDC, I'm having trouble getting it started again. I've gotten a few good thumps out of her (like 2 seconds worth) but haven't been able to reproduce.

Currently I've got the airbox off as I'm troubleshooting and I can feel and see a cloud of fuel/air mix shooting back out of the carb a good three or four inches when I open up the throttle. (again, this is while trying to start the bike, with generally unsuccessful ignition)

Was the airbox intended to catch this backblast of fuel/air? Have those of you that have switched to cone filters and the like noticed anything similar?

I know that some reversion is normal in many motors, especially those tuned for torque.
I also know that while putting the head back on it's entirely possible that I advanced(or delayed?) the cam by a tooth on the sprocket.

My sincere thanks. I am such a noob at this.

You got one tough problem there and I'll write a response mostly to keep this at the top of the list of posts.  I wonder if the slack of the cam chain taken up in the wrong direction would be enough to allow the sprocket to be off a significant amount when the slack ran out in the forward direction?  And how do you know if you are off without tearing it apart again, can't help you there but if the cam timing is off enough it will show up in a compression test. 

On the other hand the cam timing is just a worst case scenario for you, it may be something more accessible like the carb or ignition; you did take a lot of things apart. Old Fellow has considerable experience with rebuilding heads and dealing with cams.  Hopefully he'll be along with some help.

@Serowbot (new cam adjuster is still on the to-do list, this one's still pretty fresh)

@engineer (That is actually something to ponder, I didn't check the cam chain for wear/stretch because it looked pretty good and the bike has less than 15k on it. I assume that would look like catastrophically low pressure with a compression test, no?)

@verslagen1 (Instructions; we don' need no stinkin' instructions. I jest. I've been doing things the hard way and have been going off of shop manuals and intuition. Because learning is, "fun"...)

I wasn't so much suggesting that the chain has slipped to throw off the timing but rather that in re-installing the cam I'd gotten it off by a link, in one direction or the other; either on the camshaft drive end, or the cam sprocket end of things.

First thing I'd do is Prove fuel Isn't the problem. Squirt some starting fluid in,,see if that changes anything.. go easy on that stuff,,check the battery,,if it's any kind of low,it can spin over and sound like it's about to go,but it won't..volt meter time. You don't need an air filter in the mix right now...

congrats, always a special feeling when it fires up the 1st time.