I put a MC16 bottom end into my '89 MC18. Requires 8mm taken off the rear engine mount with a grinder/hacksaw:

To fit the MC16 engine you will need to grind about 8mm off the clutch side of the rear engine mount and grind the torque arm off flush. (Easier to grind torque arm off than make a spacer for swingarm to remove it) Engine/frame work perfectly well 'semi' solid mount.

Personally, I used a hacksaw and file on the cases, and left the torque arm dangling in the breeze...
Double check the side to make sure it is the clutch side. I do recall having to make an 8mm spacer after I cut the wrong side of the cases , but I can't remember if I corrected the info on my computer
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The Chopster