good point PDW, I was just gonna mention that hidden bolt too.
hogfarm, does the door rub the step or the rocker lip? was the hinge pillar or step/rocker replaced?
it is best to adjust the door to the cab without the front clip installed and without the door latch installed on the pillar (that way the door can swing closed without being drawn into a final position by the latch). get the door to fit the cab if possible and then install the front clip and adjust it to fit the cab and door. sometimes shims are needed under the rad support or the front of the cab to get the gaps and fitment right. the cab needs to be parallel to the frame (there is a dimension for this in the assembly manual) ensure the cab and rad support mounts are also in good shape before you start. there is a great video out there on doing the gaps on a 55-59. it shows how to use the driver's side front cab bolt as a pivot point to get the cab and clip lined up right so they are in the same parallel line.
anyway, sorry to hear about the body shop issues. never good. hopefully you can get it right without more painting. did the shop test fit anything before blowing paint on it?
here are few links for you to peruse if you get time and wanna see specs or how others have done it. hope it helps.
assembly manual (good to download a copy to save)
https://www.trifive.com/d1/55-59Assy.pdf
old car manuals project site, has a few body dimensions etc that come in handy. maybe bookmark the site
http://chevy.oldcarmanualproject.com...esto/index.htm
https://www.hotrod.com/articles/1304...it-sheetmetal/
https://www.hotrod.com/articles/1205...-door-install/
here is that video on adjusting gaps and moving the cab
https://www.youtube.com/watch?v=RgUwd9PdWiA