you were right. I was wrong......there were a couple of shavings in the neck pocket just like you said.....
It sits a bit better now, but I still feel like it's too high. Do you think I need to angle the neck down, and bow the neck at this point. All the measurements I have match standard neck and pocket depths, so I don't want to route the pocket any deeper. I do think the action is a bit high for me, but maybe that's something I need to get used to?
What woks said. The pickups are a long way from the strings which is why it's sounding quiet and unbalanced. If you can't get the string height lower, then the pickup height needs to come up. Both could come up by around 3mm.
A picture of the neck sitting in the pocket showing the relative heights would be useful.
Personally I don't mind high saddles on that kind of bridge. It gives you a good break angle and you don't get the height adjustment screws sticking into your palm. The only downside is the subsequent upwards angle of the long intonation screws, which I'd be tempted to cut back a bit as they don't need to be that long.
here's a couple. At this point, I've shimmed the neck pocket on the body end to angle the neck down a bit - that explains the slight angle you see. What do you think?
Some more photos would be useful - one along the neck showing the current amount of neck bow, and a close-up of the nut area, showing the nut and string height at the 1st fret.
It sounds like the truss rod could do with tightening, and the standard kit nut normally neds deeper slots or the base sanding down, but without seeing what's going on, it's very difficult to suggest anything.
I think I can't see what I asked to see. I still have no idea what amount of neck relief you have or what the string height is at the nut.
The action certainly looks high over the last frets, but those two pictures don't give me any clues about what's happening at the top and middle of the neck.
It's still never as good as actually having it in front of you, but I'd say that the neck could do with a slight amount of straightening out, so maybe 1/8 to 1/4 turn clockwise on the truss rod. However, this will tend to lower the string height over the 1st fret. You certainly haven't got any excess height there - that looks about as low as I'd ever risk going - but you may end up with some string buzz as a result. If it does, the only solution for this is going to be a new nut or live with a high action.
I always recommend setting up the truss rod first, then setting the bridge height (ideally with a capo on the 1st fret). You may need to alternate between truss rod adjustment and bridge height a couple of times. I try and get my necks as flat as I can without having any back (convex) bow in the neck - but sometimes the necks have a slight amount of twist and one edge is straight and the other still a bit convex, so you can't go beyond that. The bridge height should allow each string to play cleanly and the strings bend without choking on the upper frets. I normally lower each string until it just starts to buzz or choke, then raise it up a tiny bit from that.
Because lowering the bridge height slightly changes the angle that the strings exert their pull on the neck, then over a few hours, you might find the neck moving very slightly in response - which is why you may then have to go back and adjust the truss rod slightly - which in turn may involve adjusting the bridge heights slightly.
Once that's settled down, then is the time to do any nut slot/nut height adjustment, as you know the string angles won't be changing significantly after this, so you can then cut your slots as deep as you can without the strings buzzing. The lower the strings are at the nut, the less out of tune the first few fret positions will sound and the lower the final action will be.
Them set up the intonation. It's really not worth doing it before as the amount you have to press the strings down at the 12th fret will vary with string height - and the higher the action is, the greater the extra pressure required to force the string down and the greater the tension increase and the sharper the 12th fret position will sound. So it makes more sense to me to only set it up once you've got the neck relief, bridge height and nut sorted.
If you are struggling to get a low action after all this, then you need to investigate if it's one or more high fret(s) causing the issues. Normally displayed by one area of the fretboard where it's impossible to play a note cleanly but it's generally OK once you get a few frets either side of that area without having to raise the action very high.