So everything is back together and running... perfectly. Much better than before and it booted first time. 

Honestly, I was expecting to have issues getting it booted, but it's working well. Temps are better than ever. GPU that used to idle at 50C is now at 19C and CPU is down from 45C to 26C.

Ended up being about 7 hours of work taking the loop apart, then flushing the blocks and rads, then taking apart the blocks and clearning, then reassembling and filling and testing the loop. Still a little concerned that one of the fittings was leaking briefly, but put the pump at the lowest setting and it doesn't seem to be leaking now. Still, a container with some paper towels is under it so I know if it leaks. In which case, I'll likely buy a new fitting for it, which will mean I'll have to drain the loop again -.-

Still, the frustration was worth making my computer usable outside of limp mode again.