please don't
Move the jackshaft down... closest to the swingarm bolt you can; that way the effect will be minimalized.
(the actual swingarm bolt would be the ideal place for a jackshaft, unfortunately that's out of question on that bike.. or swingarm to be precise

)
But you can have the Jackshaft in a way, that the JS-out sprocket sits where the original engine's sprocket would have been;
You might need to fab a new brake pedal in order for it to not interfere with the JS-in... but that
shouldn't be a big deal
Also you could reinstall the original toolbox or the fender at least
since you don't have that JS sitting up there anymore
[
EDIT]
quickly made a crappy mockup...
'sid