So I bench synced the carbs with a 1/16" drill bit. Got everything back on the bike (the air box/boots were a bit of a "female dog in heat" and the clamps are a bit bent up/boots look like they need to be re-adhered but I'll deal with that later - it did all go on eventually). Started it up after a few kicks. Coughed a bit but came to life. It did dump some fuel out of one of the overflows AT FIRST, but it ran pretty well and seemed FAST compared to before. I only had time to ride it around the lot before work, but I told my buddy he could take it for a short ride to see how it felt. He said it ran pretty great, but still stumbled a bit or "lacked pep" off idle or in low rpms. He set he took it to 80mph.
I had initially set the pilot screws to 2 turns out, as per the Clymer's manual, but after reading posts on here a bit more I set them to 1.5 turns out to see how it felt the next day. It started up with a couple of kicks and I rode it home and it felt pretty good. Stalled once off idle at a light but started right back up electric (starter worked when I got it but now starter clutch seems to only work intermittently when bike has been running a bit). I went for a ride with my girlfriend yesterday and it seemed like it was misfiring on one cylinder by the end and it was back to losing power going up steep hills, at one point a loud pop and a surge.
I haven't done or gotten a vacuum sync yet, simply because I don't own a manometer. I'm hoping to have that done ASAP. Would this noticeably improve things? Should I set the pilot screws in more (I've read 7/8 turn on this forum, I just assumed I'd make adjustments in increments when needed)? There have been no more leaks since initial startup after rebuild.
Another thing I noticed was the breather hose that's routed from the engine seems to have a constant stream of whitish smoke. I wouldn't call it heavy, but it's steady. I put my finger by it yesterday and there was some oil residue, but oil is not pouring or spraying out or anything. It may have always done this, but I never noticed this breather until I was reassembling the bike. I'm not even sure how to route it, so it's hanging off the side of the frame now.
One last thing I'll point out is that when putting in the needle jet in the #2 carb, the clip was slightly bent. I straightened as much as I could, however there was some slight play left in that particular needle once clipped into the slide, whereas the others had none. This doesn't seem like it'd be an issue to me, I just figured I'd mention it just in case.