The plan has changed significantly since the sketches. I don't want to deal with all the weight and complexity of some sort of cover, so it's going to be super simple and light weight. The diagonal portion is the battery pack, consisting of 6 light weight SLA batteries. The tray that will hold the batteries will also hold the majority of the components. So the only pieces I have to fabricate are an angle iron battery tray and a motor mount which bolts into the existing motor mount (pictured below).
Maybe it not practical at this point, but...
why put the motor there? Why not in the upper triangle where the oil reserve went?
From what I see, that would significantly increase the amount of battery you could mount, especially when lighter LI's replace your current batteries. I could see the chain being an issue as it would go tight and slack more than the original chain line. Perhaps if it was mounted to the swing arm instead of the frame? No chain flex in that plan, but not sure if it is more practical than the current design.
Ideally, one could use something like this:
http://www.enertrac.net/product.php#bso there is no chain at all, and the entire frame is available for batteries.
Unfortunately, I don't think it would provide the power you need for this application, but if you were converting a 400 or smaller bike... it would work.
Or if you had one up front too... hey, an all wheel drive bike! =)