[Christ]

Paul -

If you go hooking the motor up to a shaft drive bike, then yes, it will have to be aligned. Else, no, not really.

Chain tension -

Since you're at this stage, to set initial tension for proper chain stretch, remove the shock linkage and make a center line between the sprockets, then adjust the rear wheel so that the chain is tight, like almost no movement at finger pressure. With the swingarm acting as the centerline between both sprockets, the chain is at it's longest stretch, so everything else is slacken.

Chassis rigidity -

Yeah, you need to finish any area where the engine was bolted with a cross member for the frame. The engine in most sport-bike applications is considered a "stressed member", and it saves weight off the frame by doing so, however, in situations like yours, it's a problem because you lose much of the frame's lateral bracing.

The fix is to have a machinist cut you some tubing with the same internal diameter as the mount bolts, and the length of the area that the motor used to occupy. It can be aluminum or steel, but aluminum will need to be a thicker wall.