You'll have no problems with
oil pan clearance. Just go with the pan you like.
Ford's King Cobra clutch package with their cast flywheel is good setup if you're staying below the 400 HP mark. Above that, a dual friction clutch, RAM has a good one, and a billet flywheel should be considered.
We mostly use the aluminum bell housing that Tremec sells for the 3550, but again, if you going to push up the HP, go with a steel bell housing. Tremec's TKO is also a good upgrade if you get into the 450 HP range.
My HP recommendations are flexible to the issue of how you'll drive the car. I like to upgrade on low end of HP ranges to eleminate undue stress on components. It's a little more expensive going in but better in the long run.
Hope this helps.
Boudy