CBR F3 ignition problem
 

I am having problems trying to help a friend get his bike started. Something is off and I think it's an electrical short somewhere but I want to run this by the forum just to make sure I'm not missing something. Ok, here's the deal. When I first got the bike I pulled the secondary coil caps to check for spark. There was none so I had a spare good ecu so I just put it on and still no spark. So I thought let me just check the pulse generator before I take the bike apart to get to the coils. So pulse generator good, within spec. I was checking the right secondary coil so I pull the secondary coil caps that's on the left side of the bike, there was a faint spark, purple of color. Screw it its got to be coils so I take the bike apart and pull them. The left side coil pack was within spec and the right side didn't even have any continuity on the secondary side. Simple fix, right? So I had two spare coil packs from when I converted my F3 coils to the f4i. I put them in and the bike starts like a champ and everything seems good. I let it idle a bit then began to rev it but after a while it seemed like it was running out of gas. I check the fuel supply and it was good, the problem gets worst and bike shuts off and don't want to start again. Everything seems to check out with the fuel so for shlts and giggles I check the spark again and I'm back to a real low spark, barely visible, Wtf? I switch ecu again, still nothing. The battery must be bad, so I check it and its at 12.75v. I charge it for shlts and giggle and again bike cranks really strong but, again no strong spark, just a low purple barely visible spark. I start checking around and I see that the connector to the R/R is burned, so I pull it and check the stator, which had continuity on all yellow wires and no grounding out. I have a spare R/R so I switch it and nothing changes, still no spark and still does not start. Tomorrow, I'm going to switch his battery with mine and check the coil pack again to see if they are still good. Based on my results, what's your thoughts on the problem?

BTW the problem was the R/R, even though I switched R/R with a good gone, because the wire that go into it was burned, there was a bad connection. Also the battery was not 100%.