The secondary hull on the WIP is too small and the saucer is a bigger than it should be
No, it's actually not. You're probably trying to fit the stuff you've seen on-screen to what you EXPECT it to look like... which you can't do. The saucer IS oversized relative to the rest of the ship in this "newer, kewler" version, and the secondary hull IS undersized... and the nacelles are closer together... he's got the general arrangements down almost perfectly.
The only thing I pick up that looks "wrong" to me (actually, technically, it looks RIGHT to me, but the version seen in the film is wrong, and that's what he's trying to match!) is the overall shape of the nacelles.
He's got them too "consistent." In fact, they're huge, bulbous, and they don't change cross-section nearly as uniformly as they seem to in his model. They start off MASSIVE at the front, then "blob" down to a teeny tiny cross-section about halfway back.
It looks... bad. I think his take looks better... but the problem with all the variations I've seen of this so far have been that people are trying to make the details we've seen on-screen of this new beast to fit into the PROPORTIONS of the original. This "new ship" has only as much to do with the proportions of the classic 1701 as the "Ambassador" design did.