first of all, what are using the motor for? it might not be worth it, and i have built a motor also, and the cases didnt need to be touched at all, and you use an 85-86 piston. the dome will need to be cut 2mm deeper, even easier if you have a coolhead, just call someone up and tell them you are running the 4mm stroker with an 86 piston and they will know what you need, 50$ later you have the dome.
1985 Honda ATC250R drag trike with s/t kit and full drag CR hybrid motor and drag chassis...
1986 Honda ATC250R daily rider fully modded engine, +4 swinger,etc...
1997 Polaris Storm 800 triple, boyesen reeds, dg individual silencers, 240 studs, 123mph on radar...