I imagine you have already determined how many and where the windows will be? That said IMO the windows would go in first. We started with a commercial van as it would only have the two of us inside and purposely looked for one with the only windows we wanted...the curb side slider and the rear doors. So insulating it was easy. Though we did design soft-walls into the rig rather than wall board. We really like the feel of the soft walls and marine grade carpeting throughout. Very warm and no condensation or cold spots. Obviously if we had been hauling passengers we would most likely have begun with a passenger vehicle, though the soft walls would have been the same for either.
Showing soft-wall with bubble foil insulation behind:
Best wishes on your build.
A Post Script Ramble...
On the window have or not-to-have idea (i know, out of context but thought i'd give my 2 cents worth...) IMV? Windows are over rated! We basically drive, use the "facilities", or lounge/sleep in the bed. All cooking and "camping" is done outside. So we have no need to see outside.
My wife and i live full time in a 38ft DRV Mobile Suite
. We love the lifestyle and freedom. AND we like NEVER open up the day/night shades to look out side even though most of the time the view would be fog or geese on the golf-green! IF i were to design an RV from the ground up, knowing what i know now, i would simply have a nice monitor (32" would be nice for a digital window?) with four weatherproof cameras outside that we could scroll through. Believe it or not my wife is sold on the idea too.