So, I'm feeling kind of stupid at the moment.
My bike runs hot and I've tried everything I could easily do to fix it. I ran CLR through the system, tried different types of coolant, tried running without the thermostat, and finally decided it was due to the change in fans after my alternator addition.
I purchased a couple more computer fans and was in the process of installing them, and trying to figure out how to get more clearance when I found the obvious cause. I had always looked at the engine side of the cooling system and it looked pristine. I finally took a look in the bottom of the radiator and found this mess:
I tried running vinegar for a week, changing it every other day, while riding it to work. It was working, but it didn't get enough out, and I'm not that patient. So I got me some of the hard stuff... Hydrochloric acid. I picked it up from the local hardware store. It's sold as a pool maintenance chemical. Two gallons of 31.45% ran me about $12. I also picked up a couple of shallow totes to soak the radiator in, and a bunch of baking soda to neutralize the acid when I was done.
I filled up the rinse tote with the baking soda and water first, so I could use it in case of acid splashes. Don't forget safety glasses and gloves too!
I poured the acid directly into the radiator so it ran through and out the bottom before filling up the tote. It was kind of interesting to see the acid go in yellow/green and come out clear. I added enough water to cover the radiator and let it soak for a half hour. I think it might have been a bit too long though. I didn't like how the soldered bits looked after.
With gloves on, I kept picking up the bottom so the acid would flush through the top, then laying it back down so it would fill again.
When I was done with the acid, I pulled out the radiator and let most of the acid drip off, then I washed it in the soda bath, rinsing it through until it stopped fizzing. I added more soda just to be sure there were no more bubbles:
Here's a look at all the junk that came out of it:
It cleaned the outside of the radiator quite nicely too. There were several bits of bug from the cooling fins floating around after.
I poured the acid back into the jugs so all I had left was the amount of the extra water I had added to cover the radiator. I slowly added the baking soda to this to neutralize it. It took almost two of the large boxes to neutralize the remaining acid, but eventually it stopped fizzing.
And here's the finished results:
I replaced the thermostat and reinstalled the radiator, warmed her up, then turned on the fans. Sitting in my hot garage, 86 degrees outside, the fans were able to drop the temperature and I'm happy!
DISCLAIMER: Hydrochloric Acid is some mean stuff. Do Not let it get near aluminum, it will destroy the aluminum in a violent reaction. It will eat away the solder pretty quickly and, given some time, it will eat away most of your copper/brass radiator. This was a last chance effort before replacing my radiator. I had to re-patch a tube that I had damaged and soldered earlier, but I didn't have any other leaks.