Phreakish said

If the torque converter isn't fully seated, you'll play hell getting things aligned.

If it is fully seated, the trans should push flush up to the engine and you should still have a slight gap between the converter and the flex plate. Don't force it together or rely on the bolts to pull it together!

Once the trans is against the block and you're sure the dowels are aligned, the bolts should start pretty easily.

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