If you can get your ids on a mk7 and do everything with it then I'd be leaning towards the mk6 com error being a hardware fault.
Also consider the axle change as something not available, it seems to be quite common:-(
Personally if you are in doubt take it to Ford and ask them to do it, if they can then your ids/software is crap or they also can't do it and shouldn't charge you (in theory lol) (probably will tho:-() but at least you won't lose any more sleep on it.
Also if it is locked to the pcm/central control module then maybe try and get hold of 1 from the similar van but with the axle you require, or maybe see if it is possible to reprogram your module with the correct software, bearing in mind I'm not familiar with the mk6 modules setup, would think it can't be that different in terms of installation/programing?
Failing all that maybe 13"wheels?
56 350 2.2 130ps mk7 with 2 side doors
65 290 2.2 125ps custom with 2 side doors
07 350 170ps
Ids v86 licence + v86.04 update + xprog
hereIds map
here