The other thing I've noticed is the engine management light was coming on/off and engine sort of cutting out as previously mentioned so would a short cause this?
Yes, that would be a possible sign of a short. It is not a solid, or dead, short, though, because then the fuse would blow immediately. It is just an educated guess, but picture an uninsulated "hot" wire moving around and touching bare metal somewhere. I know you re-wrapped your wiring harness (loom), but there are wires that have to leave the loom to go to remote points.
Another thought that comes to mind is to check the "kill switch" that is associated with your kick stand, and the wire(s) connected to it.
Electrical issues are often simple to fix, but tedious to find (to echo what TriumphDavid just said).