An important part I left out is the fact that it started when I first put the battery in. When I went to put the seat on I had forgotten to put the main wires to the side of the bar that holds the battery in and the wires got pinched between the seat in the bar and cut into them a little bit.
I'd say start with repairing the cut wires. Not really sure why it would run when hook to a jumper cable if it was the wires, unless the wire has too much resistance without the jumper helping the battery.
Sometimes the battery cables can get corrosion inside of them, it works it was up from the battery terminal and can cause issues with high resistance, which could explain the problem. The corrosion will be a white and/or blue powder like material on the copper wire, inside of the insulation (plastic sheath). When you repair the cuts in the insulation, expose some of the wire, ideally it will be a nice bright copper color with no corrosion,
Just a suggestion It may be that your voltage regulator is bad. When mine went bad I couldn't get it started unless I pull started it and it backfired like crazy. Another thing to look at is you may have blown a fuse when the wire got pinched it could have grounded out and caused that to happen