Coming from a builder "**** happens" the rear main seal is an art on the Fords, I have them down and haven;t had one of those leak in a long time but it happens. One reason I tend to leave them out if the person has the ability to put them in, if the motor sits the small amount of oil I put on the crank will not prevent the seal from sticking and ripping.
The trick I have found is to put a thin coating of Permatex on the outside of the seal, then slip it in...never had one leak.
Even with the one piece oil pan gaskets I put a bead across the front and rear, at all 4 corners and a thin layer on the block surface. Fel-Pro OS34508R
As far as the flywheel/flexplate goes, use Loctite (Blue) on those bolts, the Permatex or silicone will not give you a true tq reading, you can use liquid teflon as well.
The leak on Daggers car drove me insane, it was nice that Fel-Pro changed the MLS head gasket to eliminate the tabs towards the intake with out any warning or tech bullet...