Nice looking build!
The output drive sprocket to the 17 T jackshaft sprocket can be tightened by sliding the engine along the holes in the mount plate but I hit the end with one of the bolts so I can't move the engine further toward the handle bar unless I mod the mount plate and drill new holes.
Correct.
You need to modify your base and it is not uncommon.
Heck, I pretty much make all my own 4-stroke shifter bases though the SBP shift kit is a pretty good base.
Usually this involves welding a tab at the end of the front U plate the width of a muffler clamp that will fit the downbar.
The muffler clamp gives you a 360 degree grip and flat spot for mounting to.
Also did anyone blow out their nexus 3 internal hub. I don't think they are designed for motors.
No, have you toasted an internal shifter?
I have dozen or more out there and not a single failure I know of.
I absolutely love internal little 3-speed hubs for shifting bikes, the above example has a Nexus, the last one I did was Strumey Archer.
These is a simple beauty to fat chain going to single sprocket in perfect alignment.
Here is a tip for your right side chain tension...
Put a tension wheel on the base plate or via a spring loaded derailleur sprocket to adjust that so you don't need to mess with your base when it's in perfect.
Just be sure to always put any tensioner on the return side of chain drive, not the drive side, that has all the force.