I have done the non-spec measuring with our computer system also, it's time consuming with ours(Car-O-Liner). I am looking at getting Chief laser for the other rack.
I do like the ability to raise the rack up, (I'm 6'5").
EdwardSS, in addition to having the panels straight and the closure panels (hood, doors, trunk lid, top) fit and work properly, ask them about corrosion protection and welding qualifications.
They need to have all areas painted or rustproofed where welding was done. If they weld a boxed section they should be coating it with rustproofing inside afterwards. Any lap joints should have weld thru primer in the joint.
If they are truck frame shop or chassis shop they may not be familiar with the welding requirements for unibody cars. The thinner steels in unibodies are less tolerant of heat. You can't just crank up the 220V MIG and start welding.
If they work on unibody vehicles then ask to get a look at some of their work in progress. Although not a true indication of weld quality, the appearance of their welds means alot. If the welds look bad, go elsewhere.
Of course, also ask about warranty, time frames, customer visits, etc.
A walk around is a good idea when you drop the car off. Go around the car with the shop OWNER and a note pad. Make note of any defects (or lack of defects) in the paint, chrome, interior and area they will be working. This helps later on when there is a scratch in the car and you claim it was not there previously and the shop says it was. It also protects the shop in case you try to get them to pay for something you scratched a few weeks ago.
Have the OWNER sign the notes and keep it, give him/her a copy if possible.