So here's what is looks like at this point. I'm still waiting for the new 1" handlebars to arrive as well as the wheels.
The jackshaft in place but I have yet to weld it up. I have to double check the offset needed between the pulleys to allow for the shift as they each expand(one way only each).
I had to make a spacer for the crankshaft under the clutch as it was not seating against the crank. Also without a spacer the O.D. of the clutch would rub the case. There was also a gap between the end of the crankshaft and the outside of the clutch so I had to make a spacer so as not to have a 1" gap under there. I bought a larger stainless bolt and rethreaded the crankshaft as 9mm isn't the easiest to find. Really there should be only slight axial loads on the clutch as it open/closes so this bold/spacer setup is just to keep it in place while the woodruff key takes all the burden. Here are those parts and where they go.
My plans were to move the engine a bit more to the right. It felt balanced already but without those fins on the flywheel and with the pulleys as the new "meatgrinder", I decided to shift it about 1/8" to the right. I know that's not much but every bit helps get that jackshaft shorter(i.e. right shifted). I decided to remove the outside mounting holes and bosses from the case to clean it up a bit more. Here's what I removed and how the block now looks. 
