Next time/if you have the oil pan/girdle removed, trial fit the timing cover with the block clean of old gasket/rtv. Make sure the lower surface of timing cover does not protrude lower than oil pan rail. Otherwise, the girdle/pan will be forcing timing cover up slightly into dowels. This may be your cause of difficulty?

Is it a BCR /SDC girdle? If so, the block shoukd have been milled with maincaps and timing cover simultaneously to avoid
Issues like this.

In a different situation, i had to have my Jesel beltdrive cover milled slightly on the bottom bc of this situation on my lowdeck.

Just an idea to checkout.