The 4.375" bore size is the most common, mainly because there is a large and affordable selection of piston rings in that bore size. basically most of the 400 blocks are all the same (except the '71 which has more material in the main webbing area.)
For stroker engines, the cut down 440 3.75" stroke crank with 440 rods is still fairly common. Don't use the stock 400 rod length as there is not much piston selection for that combination. Most of the other stroker combinations are going to use the 0.990" piston pin size, so it it easiest to just get the entire striker "kit" of crank/rods/pistons all at one time.
The welded up 440 crank 3.9" stroker is not very popular any longer now that there are many affordable aftermarket stroker cranks. A friend still has one, but his custom pistons were very expensive.
I just built a 500 cid (4.15" stroke) 400 with a 440 source kit, and it is an easy install. The only item needing to clearance was a very small amount off the oil pickup boss. Kit clears internal oil pickup.
I have not built a 400 with crank strokes larger than the 4.15", so I'm not sure how much clearance they need or if they require an external oil pickup?
If you plan to build over 700 HP, you may be better off using one of the aftermarket blocks