Hi Peter,
Misaligned hole - I had one with my ST-1. The slight difference is not easily seen with the naked eye, it doesn't affect the play ability (that I have found) of the guitar. It only was slightly noticeable for me from the back of the headstock as I put vintage Kluson style tuning heads on, but not enough for me to plug and re-drill (the Kulsons are square at the back so when they are not aligned it looks bad. I know some of the perfectionists on the forum would disagree with me and I've added it to the list of things I will re-visit on that guitar one day but for now, the guitar rocks!
Neck bow - I've had some kits come with bows in the neck and some that are dead straight. You've got a notched straight edge so go with that. keep it straight before fret work and, personally, I wouldn't over compensate with any bow to allow for string tension. When its time to do the fret work, I would use a fret rocker (or a stanley knife blade) to check and mark any high points and low points first. again I have had a kit that did not need any fret work right out of the box! I don't have any special tools but you can have a look at my build diary for the ST-1 as to what I did with my fret work there. http://www.buildyourownguitar.com.au...?t=4399&page=5
Bone nut - I am not sure if the amazon bone nut is any good. Just a suggestion, Why don't you order a blank for Stewmac and slot it yourself? It would be a good skill to learn/try.
Fret markersAlso give some consideration to taking the plastic fretmarkers out and replacing them with MOP, if you like that sort of thing. I did it on my TLA-1R and it looks cool, relatively easy to do and cheap. Just have a look at Brendan's thread on it here http://www.buildyourownguitar.com.au...ead.php?t=2584