I did a similar original Centaur to Centaur II complete playfield swap. Specifically, the older generation used a MOLEX brand connector (15 pin as I recall) and the newer version used an AMP brand connector. So, for both pieces, I had to change the crimp pins on one side of each to do the swap.
The other thing that was different was the source for one of the flipper button lane change wires. On one, it actually came from the header plug at the MPU board. On the other, it came all the way from one of the return lane switches (as I recall) all the way back up the playfield harness, and then back down to the lower cabinet through an otherwise unused pin on one of the connectors. Obviously, EBD doesn't use lane change so this should be a non-issue.
The other thing that was an issue on Centaur was the upper arch right roll under gate. I had already shopped out and sent off the original Centaur Playfield in the newer CII style cabinet with no issues. But, when I went to put the CII style playfield into the classic style cabinet, I could not set the playfield down since the gate would hit the top metal molding strip. Not having the other cabinet to look at and compare, I ended up elongating the hole in the gate bracket to provide just enough clearance to set the playfield down. So, there was at least some kind of dimensional difference between the two Centaur playfield builds.