I tried everything to get my heater hot, no heat for a long time then it was just warm. I finally put in a new heater core (and evaporator while i was in there) for the ac. That fixed it.
I too had good flow from the core, but the way the core sits in the box, i think the bottom of the core was full of ? and not letting the hot water circulate to heat the whole core.
It now will run you out of the truck on a 0 degree day after 2-3 miles.
Check the easy stuff first as described above, keep your old thermostat in the new box for backup if it doesn't help.
The R&r of the core is about 6-8 hours to pull the dash and get it back together.
Dirk