On a budget, I'd use the cylinders you have but re-plate and stay 95mm. You can source JE pistons for about $900 including rings that work well with a GE40 cam. You can also source a set of used SC rods for about $150 and have them re-sized and bushed along with ARP bolts.
I doubt you're going to see any crank damage as it did not run long this way. I think if you're this far you may as well split the case and re-new the bearings and have the crank checked and polished. I highly recommend having the bearings and piston skirts coated at Poly-Dyne in Houston. Also have them do the piston tops with the heat coat, it is worth the extra step. It's about $300 for all the pieces but well worth it in the long run.
Lindy