I don't subscribe to the Stewmac ethos of "a tool for every job". Why use a specialised knob puller when a shoelace will do the job? I also feel that while measurements can get you in the ballpark quickly (which I can do by eye before I even start playing the guitar), the real magic setup comes from the final tweaking for feel. Most of the traditional tools are multi-purpose (my files,scrapers and carpenters pincers are probably my most used tools).
- a (set of) tool (s) to allow you to measure the string radius?
My eyes and the fingerboard as visual guide. Then play the guitar and check for choking on bends. I always end up with a slightly larger radius on strings than neck. Foster v.d. Merwe noticed that within 30 seconds of picking up my Sanox (one of the reasons why he's the only guy I recommend).
- a tool to let you measure the neck relief (even if you use a capo)?
The string and my eyes. Double checked by playing the guitar.
- a tool that lets you measure the string height over either fretboard or fret tops?
Lower the strings 'till they start buzzing and raise 'em up a little again. If it's for cutting a nut a plain old set of feeler gauges.
and if so, which tool(s) do you use during setup?
Screwdrivers, hex wrenches, nut files and a guitar tuner. A few small files (2nd cut flat and a modified 2nd cut triangular for crowning) and a few grits of waterpaper in case a spot fret touchup is needed. Oh yeah, I've usually got a fret board protector handy too (although I can do it with some masking tape).
For me, setups are pretty much like playing the guitar itself, I can spend all day breaking it down into the theory (or measurements), but I get better results from forgetting all that going ahead and doing it ...and then trying to figure out what the hell I did afterwards. Might be different if I had a Plek at my disposal though. ? Like playing, practice is important and the more you practice, the better you get at it. When it comes to setup practice, I've done a lot more than I have playing practice...