You set up index plates on the top and bottom of the box section which not only would help deal with small distortion of welding But also give you a rebated straight edge with which to create a master index edge for setting up the rails with. This also has the advantage of being able to do dis-assembly and certain types of maintenance much much easier. First you have to decide which edge is you master edge and work from that in the actual building. Though bolting works much better in most cases. This is why King bridges that are bolted together from many plates have been know to last over 80 yrs of active use.

Michael