Hey, thanks everyone for the input. I knew I was missing something on the axle, as there is a pretty good sized gap. The plate sits flush with the rotor when I press on it, and doesn't hit the bolt heads, but I will double check once I get everything all tightened up again.
I just knocked out most of the wiring (Did an all night garage one man party?). Tomorrow I am going to pick up a fresh set of plugs, finish timing and wiring along with a bunch of other stuff. Hopefully I will be starting her up for the first time this week!
I'll chime in with the results for the front wheel and calipers.
Also any hints on adjusting the calipers? I noticed that on the right caliper (when sitting on the bike) it doesn't have much play, as it bumps into the fork. I haven't done any of the shaving or anything like that to the fork lowers where the caliper bracket is bolted.
I guess I'll just see how everything works out.