In late 84 the dimensions of the head and block height of the 2R/E changed. You could have a mismatched set, but it's doubtful. Go here to help ID your head. They also have a page on IDing blocks.
Most likely you're not installing the TC corrrectly.
Here's an excellent article on TC installation.
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84 4Runner - ARBed 5.29s F&R, 4.7 & 2.28 t-cases, Chevys, AP x-over, BudBuilt x-member, 2" drv trn lift, 36" TSLs, 30 spline Longs
80 something p/u - Buick 231 V6/TH-350 trans, Holley 4 bbl, Weiand intake, dual batts, dual tanks ...
89 4Runner - stock
2000 Isuzu Trooper + 2010 Sonata
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