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When you bolt it to the flexplate it should draw it away from the bell housing slightly but stay engaged to the pump. The torque converters sit fairly close to the bell housing in those. Bolted to the flexplate you'll have clearance but only like 1/8". Let me know how it all goes together as far as the wiring. I have a 4.0 in mine against the original T18 and have contemplated AW4 swaps in the past but removed the AT wiring from my harness back in the day when I originally swapped the engine in. You can use an aftermarket trans cooler and have lines made, personally I would buy a 3 row aluminum with a built in cooler but that's just me. Cooling at this stage of the swap is the least of your worries.
That makes me feel better. Transmission is in! I still need to do axles, wiring, and other things. Although, I'm missing the stud/bolt that the dipstick bolts to. Can't find the part for the life of me. Is it a stud or bolt? Size?