I have an '06 1000RR and had the same trouble a couple years after purchase. I was able to jump start the bike when I first started having trouble, but driving home after a jump start, the dash started cutting out on me, the headlight would turn on and off, and the engine would cut out and then start back as I was driving down the road. I consulted the Honda dealer and they said it was the battery. There was an "open" (not a short) between two cells so the chagring circut was not connected, which caused the bike to cut out.
When you jump started the bike using a car battery, you completed the circuit and the bike will run. Once you removed the jumper cables, the circuit opened again and the bike will die. In the old days, you could start a vehicle and then remove the battery completely while it was running and it would remain running. Newer vehicles are not this way. They need a completed circuit to remain running.
Your uncle's battery may not have had enough cold cranking apms built into it to turn over your bike which may have caused his battery to appear to be weak on your bike. It may have even drained his batery enough to cause damage to it.
My thought, buy a new battery before you start troubleshooting the charging or wiring system on the bike. That could take days and lots of $$$.
Hope this helps.