Well... The bike is running. Though I have seemingly endless reasons to be paranoid, I think that things are going to work out ok after all.
I thought about having the crank torn down and reassembled, or buying a new assembly and sending it out to be balanced and welded, but at this point, so over budget, the choice was pretty clear: get it together and ride this thing before the growing resentment and unending money pit ends up talking me out of the bike.
That said, at .0015-.0025 misalignment, if you think about it, it's likely that even kicking the engine over will cause the crank to deflect by that amount. All that vibration shaking a 230 lb bike around? It's being transmitted through those 2 bearings. Sure, I expect that it's lifespan will be effected, but I'm hoping to get my fill of good riding out of it before having to crack it open again.
Anyways, after I finished putting it together, I turned the gas on, held the kill button and gave it 2 kicks, and sure enough, it started on the very first kick once I released the button. The bike even idles now once warmed up - something it wouldn't do before no matter what I did. I let it warm up for 5 minutes or so until the rads heated up and carefully rode it around the neighborhood for 15 min the next couple of nights. Finally last night I took the bike out to the dirt after work and after riding around enough to be at full temp opened her all the way up - insane! Instant wheel spin and fishtailing unless I sat back off the tank some, and then, instant wheelies. I'm pretty sure that the KIPS is working right, as you can really feel it wake up and go apes**t once you're in the upper rev range.