yes you should be able to run a stroker but with the 52mm from dr atv you will have to shave the skirts down on the piston so they wont hit the crank. the 50mm from classic honda you might not have to shave the skirts.
It should work, just like CMaDillac said you will have to trim your piston skirt so that it wont hit the crank. This would make for a pretty wicked sleeper motor. Would be a really killer sleeper if you also ported the head, put on a xr70 carb, and a much bigger cam in there. The stroker crank would bump it up to a 62cc motor just in case you were wondering how big it would be.
I doubt it would make the same power as a 88 kit. It would porbaly have around the same torque as a 70cc. I could be wrong though, ive never ridden a stroker motor. I just dont think it could make any where nere the same power/torque has a 88.