I finally built my Reloaded MK2, and I'm having the same problem. After reading about this problem here and on other forums, and after some experimenting, it seems like the best solution is to just install a quiet fan inside the case. When I aim a fan at my case the problem goes away, and others have reported the same.
I don't have the soldering skills or tools to solder that resistor, and I don't know where I'd find anyone to solder it for me. I can solder, but not something that small and delicate. And one person says that the resistor change caused problems with PAL mode, and I don't want that. The fan seems to solve the problem without creating any new ones, and it will also keep my old C64 chips a little cooler.
So my question is, where is the best place to tap power for a 12v fan? I could maybe use a 5v fan if that's preferable, but I already have a quiet 12v fan.
And is there any place on the MK2 board where I can safely drill two small holes to mount a 40mm fan on stand-offs? Ideally I'd like to mount the fan to the MK2 board on approximately 2-3cm stand offs so that it's raised up near the case vent to force air out of the case. I could maybe figure out some way to attach it to the case, but there's no obvious way to mount it, and it seems a lot better if it's mounted to the MK2 board so that I can easily swap the whole thing to a different case without having to remount the fan.