you cannot use a auto flywheel, coupler bolts to the clutch bolt holes, yes you are going to need to disassemble, if you don't it will...

Years ago I built a 496. Balanced my machine shop. Started it and it had a vibration at 1,200 RPMs. The pin to line up flywheel was removed and I lined it up wrong. Never make that mistake again.

If you didnt get the rods and pistons matched to the stroker crank its highly unlikely the rest is going to pan out on the external side.
On the oem gm side there are subtle bobweight variations based on which pistons used ,within the same crankshaft casting numbers , then there are are revisions in the flexplate balance based on that.some builders can make calculations based on the crank pn the rod and piston weight ,then mod the flywheel and balancer alone to make it work. If you have the part numbers to rods and pistons too ,that could be path of least resistance

Wd1548-060 pistons
41253 pro comp rods