I believe the body and front suspension were the main differences. Engine, trans and a lot of other mechanical was the same but traditional bodies had the Safe-T-Flex suspension with the center link steering layout while Clippers went to the more conventional lower A arm and steering linkage setup. The Clipper also had a rear transverse shock absorber which I don't think the conventional bodies used.
If you want to compare detailed mechanical specs the 41 conventional models are in the Sept 15, 1940 Service Letter Vol 14 #17 and the 41 Clipper is in the April 1, 1941 Service Letter Vol 15 #7. Both can be downloaded from the Literature Archive, Service Letters, Counselors and Bulletins category.
There is another publication with more detail on the
Clipper body differences.
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