I assembled the CV joints and installed the axles today. The boots fit okay despite the larger diameter axles, although I won't be surprised if they develop cracks sooner than normal.
The picture on the left shows the original Miata axle on top, and the new axle from Dutchman Motorsports on the bottom. To the right is the assembled axle with CV joints.
Installing the axles went pretty well although I did need to "customize" a socket to get to the inner bolts. I expected to have to remove the uprights to get the axles in but since the inner joints slide I was to work them into place without taking anything apart.