this is interesting indeed.
i've had three different engines in the '66 i have. the latest engine is from my old pony and is a '65 block. my dad and i had no problems getting it in using the '66 motor mounts. before this, we had a 289 from a '64 fairlane in there and that too fit with no problems using '66 motor mounts.
with each swap, we did not have to do anything to make it fit right. what you mention should work fine. if it's possible, do you have a pic of what you did and of the mounts?