Thermostat is still not leaking, and replacing the heater pipe solved the other leak of course. I wish people didn't mangle those in junkyards while getting the intake manifold, I could only find one in tact in one of the local yards.
I flushed out the system even more today (circulated 10 gallons of water, it's still a little rusty, but MUCH better than before) and vacuum filled it with coolant and distilled water. That was after I ran it for a few days with Blue Devil cooling system flush additive. It seems to have loosened things up a bit, the chunky rust paste in my radiator cleared up quite a bit once I put the hose in there!