The rear main seal is put around the end of the crank. It fits bewteen the last main cap and the block. The oil pan...you either use the 4 piece, or the 1 piece. You are probably mistaking the rear piece of the oil pan seal. The block determines weather you use a one piece or a two piece rear main seal. Front sump for 289/302 oil pan will work.
The direction of the water pump is going to depend on what pulleys you use. The rotation of the crank is clockwise. If you are using late model accessories, serpentine, you can, but don't have to, use a counter clockwise rotation water pump. That's the nice part about it. You get to decide.
I don't recall right off hand which way the engine turns It also depends on what side your looking at it also. I DO know the distributor turns counter-clockwise. And that the std rotation is what you need. A reverse rotation waterpump turns the opposite direction of the crank and thus requires an additional pulley to reverse the belt.
Thanks guys, you have helped me alot. I still have some questions about the finishing details of my engine build. I need to sit down and organize them, and when I do I'll be sure to post them up.