Hi All,
Since I had to replace the stator connector anyways, I went ahead and soldered the connections in hopes it would remove any opportunity for this to happen again (I had a bad connector). To prevent this from happening to you; use de-electric grease on the stator connector annually (you've been warned)!!!
This was a big project, though if I had to do it again I would now move much faster knowing the process. A few things I took away;
1. when pulling the engine free of the UJ, be sure to slide the UJ back (there's a bunch of room gained by this)
2. Definitely align the cams and pull the right hand pully, and also the pickups on the crank, such that they stay with the frame.
3. Not quite sure where the 7 wire lead's connector is that goes to the bottom of the engine, so I ended up cutting it and then resoldering it. This did not make me happy, though I got over it.
4. You'll most definitely want to order a new stator, rear cover seal, clutch seal, and maybe o-ring seals (4) for the carbs and for the water pump and thermostat. You may not need the o-rings, but better safe than waiting for them on a parts order.
5. When screws are pulled to removed a cover, fairing piece, etc., stick them back in the hole they came from, or place them in little piles of parts so all stays together. Doing this I lost no screws or parts.
6. Getting the engine back in is a pain in the rear; would love to know the magic trick!
Doing the stator replacement was a lot of work, but in the end we saved a ton of money and I got to know our new/used bike better then I would have otherwise. We bought the bike cheap because of this issue, then did the work ourselves, thereby giving us a reliable new toy.

It now runs great!
Thanks VMSGuy for your help, and Steve for the great videos and instructions.
David