Jacob,
Pardon my ignorance here, but why did you need to notch the case? I'm in the process of assembling a 660 from parts with a BB kit. I've had the piston and cylinder on without rings to check squish, and the piston cleared the cases and one of the two base gaskets that I've tried. The thinner of the two Baileys gaskets didn't clear, and the thick one makes the squish .050". I'm waiting for some Stihl parts sourced locally, including base gaskets. The .5mm Stihl 064 base gasket that I do have clears the BB piston skirt, but obviously, the bolt holes are off location.
Every 650/660 I've dealt with on these NG BB kits wouldn't clear the 56mm piston when at BDC. Now that doesn't mean every 064/066/650/660 is that way. Almost every first gen. BB kit I used I didn't do any case notching.