1 The degree just refers to the lifter bore, correct, the rest of the block is the same?

Yes

2 Are there different heights of the blocks?

Yes, 8.800"-9.600"

3 Are all 48* blocks 340 mains?

Not sure, most all 48 degree blocks will be 340 main but may take a 360 pan depending on the rear cap used.

4 Which of the 48* blocks are best for procharging?

All are great but the R3 with siamesed cylinder bores and 18 head bolts is the strongest. 9.600" deck is prefered to give more room for a dished piston with stroker crank.