Dont cover the hole in the block, it doesnt go anywhere anyway. On mine I used the rubber gasket and a bead of silicone on top and bottom, hasnt leaked in 3 years.
There was a write up about it in last months 5.0 Mustang and Super Fords. Im thinking about picking one up.
To me it sounds like an alternative to welding your axle tubes.
It might get a little lighter as it wears in some during the breakin. You shouldnt have to adjust the shift stops unless your shifter moved a lot from when you reinstalled it. Sounds like you just need to adjust the cable/firewall adjuster some.
Any vacuum line under the hood that goes to the intake more or less. I used the one going to the fuel pressure regulator. You should be able to tap into one on the vacuum tree right by the drivers strut tower.