Some of the valve size issues will work themselves out under boost. When the door opens the wind will rush in. That thing turning 2500-3500 RPMs will be a beast.
For a standard OD tranny that is tough I'd consider a Borg Warner T 85 with an R 11 over drive. These were used in Studebaker Golden Hawks (supercharged 289 V8) and Ford pickups. The T 85 is what ford patterned the 4 speed "Rock Crusher" after.
When Ron Golden used the Hudson rods in his 302 GMC the gig end had to be narrowed to fit the GMC crank and the crank was ground to Mopar flat head spec so Dodge rod bearings could be used. The Hudson rods are 8". It is interesting how many old race cars used welded rods.
