If you've got as far as realizing that its a few millimeters that makes all the difference, then you truly have all the understanding of the situation you need. After that, its trial and error.
When I was putting my truck back together (after swapping chassis) I bolted down the tub and then installed the bulkhead, doors, and fenders based on that. In the end, I feel I should have installed a spacer between the tub and mounting tabs - just a couple mm's would have been great. As it is, I have to shim my door strikers out farther than I like. The number of washers used between the chassis and bulkhead is trial and error.
The primary mistake I made was assuming that it would be OK to base everything off the tub position. In fact it takes more finesse and ability to finely position the panels.