1997 yamaha yzf 600r electrical problems

After you change the main relay check ignition fuse from your fuse box.

Check your coils ,check your oil see if it has water in it ?clean your tank add new fuel ,check all wiring like huttner899 said .check compression on cylinder head ,hope this helps

A jump box is nothing more then a battery with leads on it so where are you connecting it verses the new battery you put in the bike. that doesn't make since unless you are connecting the box right to the starter motor then it be constently running the motor untill you unhooked it. check all your fuses and examine all wire harnesses for damage, burns, or any mellting.