You don't need "custom" pistons per-se. Many companies make an off the shelf stroker piston. If you went with the 94mm stroke, you'd either have to use those off the shelf stroker pistons with 3mm longer rods (correct me if I'm wrong on the measurement, but they do need to be longer). Or you could use stock length off the shelf rods and have pistons made with a wrist pin height somewhere between 2.0L and stroker 2.3L ones.
As far as grinding the block, don't worry about it, it's really not hard to do, and I'm sure your machinist is capable if you don't feel ok with it. I couldn't tell you if you would still need to grind with the 94mm crank. I'd assume so, because I think I removed a bit more than 6mm from the main caps. You probably don't have to clearance the #3 cyl because that was only minor grinding necessary.