No, we didn't need to do anything to the crankcase area in the first engine that was built, but the A13 rods that were used had a larger than usual piece on the side to direct oil onto the bore. It became necessary to notch the bottom of the bore slightly with a chain saw file, on one side only, to clear this protrusion.

Strictly speaking, this part of the crank does not need to be modified as it does not intefere with the piston. It's really only the counterweights that pose a problem & the machining is done to clear the bottom of the piston at BDC. You could run a stock A14 crank if you modified the bottom of the pistons instead.

In this instance, we chucked the crank in a lathe & just turned it down along it's full length. To determine the right size, just fit a stock A12 rod & piston to one crank journal. When you can rotate it around the crank for one revolution with a small, but realistic, clearance between the counterweight & the base of the piston, then the crank has been reduced enough in overall diameter.

Before doing a final balance, just mock the engine up using one piston, without rings, just to be sure it all works right.

It looks like you took off about 5-10mm.
What about the big end of the connecting rods? do you have to grind the block to clear them as well?

Only a smidgin comes off the webs & the journals are never in danger.