I'll reserve final judgement until I see what you have planned, but I don't think you're going to be able to replace the OEM heater core with anything other than a similar replacement and have it function like the original. Finding one that will fit in the existing housing is key, otherwise air leaks will reduce it's effectiveness. The hose routing is very likely done the way it is for a specific reason, however illogical it may seem. If you can engineer a system better than the Mitsubishi engineers, I'll be amazed and impressed.

95 Montero SR
3.8 MIVEC, Advance headers, 2 1/2" exhaust, Magnaflow muffler, OME shocks & rear springs, 2" body lift, 3" tank lift, 4.90s, TRE front locker, factory rear locker, Roger Brown Rock Sliderz, 315/75r16 (35") tires, Sport big brakes