Hi--I danced this dance last year while building my roadster pickup. I was using new glass fenders and boards, and since none of the holes were in them for mounting to the original frame, it was hard to know where to start. I finally found out that to get the correct positioning relationships, first you have to mount the grillshell and the chin apron that fits below it. Those positions are fixed, and can not really be altered. The positioning of those two items dictate where the front fenders are positioned, and that determines where the running-boards and splash aprons are located, and that dictates the position for the rear fenders. If you have lived a good clean life, and are very lucky, and have not altered the wheelbase, the rear fenders should be centered on the rear wheels.
If you start at the rear fenders and move foreward with the installation, you can end up in a mess at the junction between the grillshell, chin apron, and front fenders.
As far as the sequence for tightening the bolts, tighten everything a bit at a time, use a rubber mallet if you have to do any minor persuading, and try not to torque anything down the first day---bring everything to semi-snug, then go back the next day, (even better in 2 or 3 days, and tighten things the rest of the way. If the fenders and /or boards are glass, use nylock nuts on the bolts and use a fender washer under the bolt head and under the nut, and don't torque things too much, just enough to close the gaps.