One thing to check... The heater hose / control valve on the firewall is the highest point on the cooling system and it will airlock the heater core if you don't bleed it.

With the engine COLD and running and both front and rear heaters set to hot, loosen the hose clamp on the contol valve hose and pull the hose off the valve a bit until coolant comes out. This fixed the same problem with my '89 after a rad swap as there was just too much air in there to flush out.

1989 4Runner Special Edition
22RE, 5-spd.
TG 3" SAS, MC DuaLs, 4.56s, Air Locker
Hi-Clearance panels by
www.toyotafiberglass.com