When I first got my Samurai in the spring of 2000 I installed a brand new stock heater core and it always cooked me until this year (it sat outside uncovered from 2004 till 2010 so it was way clogged I cleaned it out last month and it works great again).
A few questions for you, is much air blowing through your heater core i know you said you cleaned it out already but could be other problems like a bad blower or blower switch, is there a clog in your coolant lines maybe one right at the valve, is your engines thermostat working correctly?
Only problem I would think of with doing a heater swap would be fitting it either the whole heater and blower assembly or even just the core itself, might be able to find one though, if you can look through a junk yard to see what may fit I think that might be easier then looking somewhere like JC Whitney because with them I think you would need to put in a make and model first before it shows you anything.
