Well, here's what (as far as I know) should have been done, at least as a general rule of thumb for this. The tuners and the strings should have been taken off (and new strings put on at the end, but in the big scheme of things that really isn't a big deal). The neck repaired. Then the finish around the area sanded off (maybe even the whole neck since it's a transparent finish that gets darker the more you put on). Then the best way to do the new finish would be to spray it, to try and keep an even finish on it. With the runs he should have at least sanded them down, and like the everyone said, the fretboard should have been taped off and there shouldn't be anything on it. As well as that fingerprint you just mentioned, that's just sad, I would hope anyone would clean glue and finish and whatnot off their hands before they touch an instrument.
As far as the finish color, it might be difficult to get an exact match, since even the thickness of a transparent finish affects it's color. Just a thought.