Here is some insight I can offer to all from being on the other side of the counter as a body shop manager. And please excuse me for some rambling as I'm working on a big Bloody Mary after knocking off for the day.
When you work out the details with the shop of choice, DON'T say you are not in a hurry[ or that you need it by the end of the week/month]. It will be on the perpetual back burner or look like poo. Work out a schedule for completion and keep in mind any changes/discoveries[rot/bad previous repairs] will extend the due date. Drop by periodically unannounced to see how the job is going. Don't just cut a check every week and not see what's been done to warrant the payment. Do you want all of your gaps perfect and body lines matched? More time needed which means more $. Don't want to see waves down the panels? $ again. Want the jambs done too[ which burns up almost as much time as the outside panels]? More dough! Be realistic about your expectations for the finished product too. Are you driven by money outlay only, many are, or perfection? Many people expect a Goodguys top tier job for less than a grand. Get real! Paint jobs are just the top layer of the body prep. If the work underneath is bad, the paint ain't gonna hide it. Slapping more mud onto an already bad job is not going to work for long. Same goes with paint. If the car has been painted multiple times and has paint issues going on, you need to STRIP IT, not put more on. Again $. Our cars are old and have been repaired and worked on before. Expect surprises! Count your blessings if its pristine. Many people are driven by cost alone on body work and painting. They have no issues with dropping big bank on an engine/trans/bling wheels etc but whine about the body/paint costs. When I managed the shop, 04-07, just the paint materials to do a complete paint job using PPG DBC base was 4 grand for a musclecar size job. Top quality materials that last more than 5 years in the open elements. The 4 grand is materials only! Yes you can buy materials for less than that but they don't last as long. Repair labor, detrimming the vehicle[ removing mldgs/trim/handles/glass etc] is on top of that. Add to that the cut and buff after its painted. 2+ days there. $. One big area you can save some money at is to take the car to them all detrimmed[ lights out, trim off handles removed, bumpers removed etc, car is clean/no road grime, glass pulled etc], plus you get a better job this way.
Old cars need to be looked at like old houses. You make a purchase and decide to paint/repair/upgrade etc. Pull the drywall off, remove gutters for paint, take care of a little dry rot on the siding. You get in there and discover OMG! Its worse than it looked. Now you are in for some fun and must do repairs to do the job correctly. You could not see it from the outside but once you got things cleared out it was surprise city. Same goes for cars homies! The shop people don't have x-ray vision. Out here we could only legally put what we saw on the repair order and could not make guesses. The only way you'll know truly what you are up against for repairs/paint is to STRIP the car, therefore getting everything out in the open. Of course by that time you are truly committed to the work.