I love this guitar. It has a really great feel, sound and electronics (minus the wiring, that is phase 2 of this journey) for the little bit of lead work i want to throw into a recording. I haven't really played it much as it just always seemed out of tune with all my other guitars, so it rarely ever makes an appearance ever. It just had some nasty intonation issues working against it. I set about giving it a good going over using some basic guidelines of a good pre set up inspection and two things stood out to me. A: The neck needed one heck of a truss adjustment. B: Based only off internet research and talking to the guys here, the nut slots may have also been to high.
Acting on advice from mutt i got the balls up to do my own truss rod adjustment to kick this off. I didn't want to. I think in my teens and early 20's the local shop had me scared to death to even look at the truss rod. I am a grown ass man now and common sense told me i SHOULD know how to do this by now. I didn't force this leg of the journey. I took my time. I think at most i did like a 1/4 turn and let it sit over night, then checked it when i got home from work that night and adjusted it again. Rinse lather repeat. (I was actually doing this to two other guitars as well) I ended up cranking around 3/4's and +/- an 1/8th of a turn on the last night and it got it pretty good. That alone helped some of the intonation issues a bit but every string was going hella sharp when i capo'd the first fret. I adjusted the saddles at the bridge at this point and it made very little difference. Some difference but every string was still quite sharp so i conferred with mutt again and he felt pretty confident it was the nut slot heights and advised me of an ideal height re: the height of first fret plus a bit of headroom. Another source also made the same suggestion.
This nut wasn't even close. I picked up some feeler gauges and measured out the height of the first fret. Added in some extra height into the measurement for some clearance over the first fret and this is what it looked like.
Each string had pretty much the exact same gap after that except the little e string. That guy was a little closer but not a whole lot.
I went and bought some welders tool tip cleaners to do the slot filing on the cheap. I had read on another forum that some guys have had good luck with these things when in need and do a decent enough job. One fellow added that they had good luck with them but they were PAINFULLY SLOW GOING. He wasn't wrong. After about an hour i managed to get the slot lowered a bit. These little files did a tidy job given how fine they are and how little material (bone in this case) they removed.
The photos look a little misleading and that perhaps not much has changed. It doesn't really look like it moved much but it did. I also didn't go right to the feeler gauge in that last photo as as i snapped the picture i realized that i when i added in the extra bit of space for the gap i only added 0.002 of an inch instead of the recommended 0.020 of an inch.
So i just left it right where it was. If anything it is probably a bit to low but not in a bad way? It seems to be in perfect intonation at this point. I did add in the correct gauge to the stack after i snapped this photo i just forgot to take a pic of it. It was a pretty snug fit under that big E string. Whoops. 
I'll spare you pictures of all the other strings but i will say the 7 dollar tool tip cleaners only afforded me the ability to adjust the slots for the E, A and D strings.
I wasn't going to try to use any other gauge size for the small strings. I had flash backs to a shitty Yamaha our family used to have and the g and b strings were for ever popping out of the nut so i wasn't going to go there. I had read elsewhere you can fashion some crude files out of feeler gauges with the help of a dremel but as i was explaining that to my buddy at the music store his boss overheard and was like "no dude, that is way too much work i'll just lend you my nut files" He kindly agreed to bring in his own personal files into the store for me to pick up the following day.
Worked great. Maybe a little too good because i am pretty sure my b string is a little lower now than it should be. It buzzes every so often on the first fret. I am sure when i restring this and readjust the action to compensate for the lowered nut now, that buzz may correct it self a bit. Long story short, I am going to add these nut files to my various wishlist's and keep an eye out for them and their respective sales.
So now the slots are good, the intonation is much better (i wont really know EXACTLY how much better until i get new strings and really good set up done on it) but it is way better than it was holy jesus!!!
The only problem now is that the nut was just looked wrong and i started to panic. 
Then i recalled [mention]muttley[/mention] mentioning to me that 2/3'rds of the string should be seated in the slot and the other third above the break point kind of thing. After looking at all my other guitars sure enough thats the way it should be. I had some more work to do.
Luckily i had a bunch of cool files i bought years ago for carving shit out of soap stone and they sort of came in handy for reducing the headroom on this nut. I suspect i am going ot make mutt cringe a little bit with the following text but i just eyeballed this part of it. I took my time. Probably about 2.5 hours but i just filed it all down flat right above the D and G strings until i hit the top of the string, and then started just spreading the radius out towards where the E's live. After i hit those strings i took all the strings out of their slots and then started to file it down a little bit at a time, put the strings back in their home see how much was in the slot and how much was out and either carried on or stopped.
Once i was done with all that, i colored the whole top of the nut in with a pencil and started removing material off the back toward the front holding the angle of the head stock. Once happy with that i went over it with four different grits of fine sandpaper and it polished up pretty good.
Self Analysis:
- - I should have put some masking tape on the fret board side of the nut while working. Idiot.
- I think i over did it around the big E string. I think there is more string showing above the nut then there should be and i definitely over did the stupid little curved rounded corner i put on there. (Please don't ask me why i rounded the corners? i just did! my brain said do it so i did it!! shut up!!
) You can see it drops off way more than the little e side. It seems to be seated in ok. I gave it a few good Shan whacks on an open E minor chord and it stayed put so i would say it's fine.
- You can also really see how the b string is slotted a little lower then it should be. But whatever. The guitar is in tune now and i love it. I don't cringe playing an A minor anymore.
It could definitely be better no doubt, but for a first attempt i feel OK with it. It is definitely a different feeling guitar in a good way!! That makes me want to play it. real bad. To me, that is mission accomplished.
Next up is fix the shitty wiring rat nest living inside the cavity. Wish me luck and stay tuned.
