I *love* this project! I had an Ergo 4000 for about a week a while back. I loved the layout - I'd tried MS's previous ergo boards, but they were nothing special. The Ergo 4000 had a pretty amazing layout - not radical, but obviously and immediately better feel than standard keyboards.
However, the key switches & keys themselves were horrendous! I might have even stayed with a non-mechanical had it not been for the keys. The spacebar was the worse, but most of the keys had binding issues.
This project would solve the worst of the problems, which is awesome.
Any updates? I'd love to see how you did the insides, how you mounted the keys, etc. I'd definitely consider doing this with some Cherry switches if it works out for you.
I'd also love to see how the old modifiers & spacebar could be kept. The old modifiers were strangely shaped - very large & slightly flatter. The spacebar was awful - tons of flex, very large, only one switch in the middle with no stabilizer bars (?!?!). I'd split the space bar into two sides, a switch for each, and just wire them to the same contacts. You could avoid binding, and still keep the good shape of the key.
I would imagine that replacement standard-size modifier keys are going to be harder to press, since they're much more spaced out.
Good luck... updates! Pics! We demand more!

(PS. Also, a review of how it works now and your thoughts/feelings so far would be awesome)