Engine swap

OP, just a thought: Is there a shroud there that you cannot get the fan and clutch past? If so, then loosen the shroud and pull up, put in the fan/clutch, and drop both shroud and fan/clutch in place and tighten them up.

I wonder if you had old sagging mounts before, which lowered the engine and let the fan/clutch come out past the shroud before, and now you have the engine sitting higher with new mounts, and that 'gap' under the top edge of the shroud has closed up.