You're not going to believe this, I
very recently went through something exactly like this. My car was running hot after the new engine so I upgraded the coolings system with a griffin rad and black magic fan. It still ran hot.. even hotter than before. I changed the thermostat a couple times(aggrevating with a blower on) and I kept trying to figure it out. Long story short.. the black magic fan was blowing the wrong way!! It was wired wrong from the factory! It felt like it was blowing in the right direction when you put your hand behind it because it was blowing against the radiator and then back towards the engine. We dropped the fan and switched 2 wires and now it runs so cool... its perfect.
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Rick
My 89lx(updated 7/20/2001)
My 97 Cobra