sboubel,
Definitely powdercoat the frame. It is more durable than painting. If you plan to make any modifications to the frame (detabbing, bracing or mounting an oil cooler), now is the time to mock it up BEFORE powdercoating.
As for the motor, you did a nice job of cleaning the cases. Too bad you skipped porting. That would really take advantage of the increase in displacement and cam by improving the intake flow via your brand spanking new valves. It's not TOO late, but you will ended up removing the valves and reinstalling them to port it. I would do it now while you can. This will really wake up the motor. You should also port the manifolds to match.
The bike has a little bit of wear and tear but it was in damn good survivor shape. It looks like it sat garaged for most of its life. What are your plans, aside from the engine rebuild? Are you keeping it mostly stock?