What is your budget? If you are looking for something a little more industrial, try Haas CNC. I use one at work ( I'm also starting to do some guitar work on the side) I love this machine. We've had it for almost 7 years now and have not had a lick of trouble. We have a VF-3 which is big enough I could cut neck through guitars if I wanted to. But Haas has many smaller machines as well. The control is very easy to use and learn. With one day of training you could be programing and cutting parts. The only thing is they cost alot more than a shop-bot. It all depends what your want to do.
One other advantage of a more industrial type of machine is a tool changer. I was just rereading your original post, and it sounds like you want to do several different operations in you machine. With a tool changer you could set up a fretboard, cut the fret slots change tools cut the inlays, change tool and cut the taper, and you only set the job up once. If you were doing runs of say 10 fretboards you would have 30 maual tool changes. With the tool changer you set up the job once and from there you put your board in the jig and hit the green button.