If there is truly no damage to the piston walls, and it is fairly low mileage since it was rebuilt, replacement pistons should work O.K. Just make sure there is no damage to the rods as well.
The tailshaft housing needs to come off. You will have to remove your shifter as well and drive out the roll pin that holds the shift block on the shift rail of the tranny.
It will as long as you don't beat on it too hard. I've been running 11 lbs on my stock shortblock with 100,000 miles on it for 2 years now, and it's been down the track at least 50 times. I launch at about 4500 rpm and the clutch (unknown) and stock tranny are still hanging in...for now. I lost...
I've always liked the Motorcraft (Ford) batteries, but I've heard good things about the Optima as well. I think I might try one next time I need a battery.
I'm sure any place that sells parts can get the pushrods. They don't necessarily have to be TFS, just make sure to order the right length, and order the hardened rods if you are running, or plan on running guideplates.
They are both 8.8's but I'm sure the explorer rear is wider and has different mounts. The gear sets will interchange though, and I think a lot of Explorers came with 3.73s.
They make an assorted variety of grommets, so that shouldn't be a problem, try an autobody supply shop. As far as the one in the brake booster goes it shoudn't hurt anything... until it dries up and gets sucked into your engine.