I don;t want your post to go unanswered. Yet I cannot really speak with authority..... and thus am reluctant to answer because to do so would be more speculation than not.
I am DYING to get my hands on a 5R55W/S or N. I think a 5R55E frankentranny could be born!
So as for the differences, one needs to understant that the C-3 became and A4LD, became a 4R44, and then a stronger 4R55, then a 5R55E, which became the 5R55W, and then the 5R55S and N, which still are in production today (W,S and N.)
One major difference was the fact that the W,S and N have unitary cases.... no separate bellhousings. Bolt up problems ? maybe. Little leeway.
The computer setups I imagine will be the biggest problem in a swap.
Not suire this helps... but I am willing to bet a set of W guts "might" fit into an E case..... for me, that is the next area I want to inquire into.
ps. I will post a thread on my thoughts for tranny/transfer case projects for this winter, and ask what people want to see first and might support. ("Support" = eg. selling the virtually "new" 4R70W trans I am building in that Diary - which I did..... ) Another example.... a pre-sold "new" frankentranny, or if possible ... a 5R55E/W frantentranny ...helps the projects along the way monetarily....because I usually only hope to break even on the first one of a "diary" if i am lucky. And that is not including the time it takes to do a Diary.