I researched taking the heater core out of my car for a while. What I found (at least with 1g's is that if you just block everything off, the coolant can no longer circulate unless you loop the lines somewhere. Might not be your issue, but worth looking in to. For me, I decided to just keep the heater core, wasn't worth the hassle of saving ~10 lbs.
http://www.dsmtuners.com/threads/que...r-core.426104/
http://mitsustyle.com/forums/showpos...&postcount=131