I'm also thinking if I'm changing the rear seal, it's probably a good time to change the clutch while I'm at it. What do you think?

Not an uncommon issue, but don't know how common it is with modular engine.
It's the best time to replace it seeing that you will already be there.

That sucks. If its a rear main the trans has to come out and yes it would be a good time to change the clutch. It could also be a pan gasket so it's worth getting checked out.

Any time someone changes I always suggest to change both the release and pilot bearings at the same time and if its not too expensive the fork. Then everything is new and ready to go. While you are at it an aluminum quadrant and firewall adjuster would be a good idea too.

I know you we're talking about forced induction down the road so it would be a good idea to go with a beefier than stock clutch. Lot's of people use the Ford Racing King Cobra and there is a company called Valeo that makes a very similar clutch. The story I have heard is that Valeo builds clutches for Ford Racing but I can't 100% confirm that.

^^Thanks for all the info Chad, I will most likely be going with a supercharger of some kind (when I can afford it), so I will likely change everything, including upgrading the clutch. I was going to attempt doing some of the work on this car myself, but this time it will have to go to the shop, as I'm lucky to get 10 minutes off work these days.

No problem. Sometimes it's best to put the time in at work and pay a professional to do your repairs. Trans removal on the floor is a pain especially without the right tools.