Isherwoodc, first let me congratulate you on your first guitar. Looks good and sounds like its got the potential of playing OK. Before I try to comment on some of your questions I'm going to go back to square one and define a couple of terms.
First is what I call DESIGN - thats where it starts. Basically that is the general type of guitar I'm going to make and some specifications that I choose pretty much at the start of the project - scale length, neck width at nut and some other place (usually bridge), the fretboard radius. I'll decide on the neck connection and probably pick the bridge I want to use. Everything else after that becomes DETAILS (wood, pickups, finish, yadda yadda)
Next is GEOMETRY - very simply that assure that the neck and bridge will work together allow the ACTION to be set reasonably. Geometry varies from guitar to guitar but basically it says that I will have enough adjustment in the saddles to allow me to make the thing playable. Included in this is the angle of the neck to the body (zero, positive or even possibly a negative angle), the amount the neck stands proud of the body and takes into account that the f/b radius needs to be duplicated at the saddles.
Next are the FRETS. I'm anal about frets - if they aren't perfect there is no point in going on. High frets, low frets, worn frets - any problem with frets will mean compromises in the playability.
Last is the ACTION - that is the relationship of each string to each fret so it will play easily and comfortably with minimum or no buzzing for my style of play. In my book action consists of things that can be changed after the guitar is built - relief, height of strings at several points on the neck (nut and 12th fret), and intonation compensation. While not really a part of action, I include adjusting the height of the pickups here.
I'm a hobby builder and repair person and when a guitar comes into my shop before I do anything else I measure EVERYTHING and write it all down. I have a little spreadsheet that has boxes for neck angle and fret condition and whether (and where) there are buzzes, neck relief, nut and 12th fret string clearances, amount of compensation (and how much the intonation is off). I've even got boxes for string gauges (you'd be surprised how many people don't know whats on their guitar).
It takes me all of 5 or so minutes to measure and fill this stuff out. I know exactly what has to be done and the order, since some things affect others. The spreadsheet also has little boxes for target values (varies with guitar and player) and when its all done, for the final measurements. My point is that before I ever take the string off or turn the truss rod or anything else I have a plan. (If you wanted to PM me your e-mail addy I could send you the spreadsheet).
If I were in your shoes, I would use this guitar and experience to study and learn each of these items. Personally I would stop right now and do the measurements - write everything down. I would spend some time analyzing the geometry - does the neck angle allow you enough adjustment of the saddles to go from the lowest action you'll ever want to the highest (for each string). I know that the lowest I would ever want to go is with the strings sitting on the fretboard - therefore the neck angle should allow that
Thats a ToM bridge, different from your but the idea is the same. The little wood blocks simulate the posts that it mounts on. What I am doing is setting the very lowest adjustment at the fret plane. Actually I know that when its strung up there will be a little relief plus the nut slots will raise the action a hair.
The other thing you want to insure is that you can adjust the saddles as high as you ever want them. Lastly, you'll want to remember that as the guitar ages the action will go up, you may want to fudge a little to know you can compensate.
OK, get the geometry right - you may have to shim the neck pocket (one of Leo's genius's) and go on to the frets. Adjust the f/b dead flat (take all the relief out) and level the frets. There are lots of tutorials and methods - your goal is first that they be perfectly level and second that they have a reasonable shape (rounded crown).
Now you can put strings on it, adjust the saddles so you have some clearance and do the setup. The steps are pretty much as follows - some adjustments affect others, some do not. Measure and adjust the relief - different techs have different values that they shoot for but basically you want some but not too much (LOL). I shoot for 0.004 or so with pretty perfect frets, I think anything over 0.010 is too much. Remember that adjusting the truss rod will change both the relief and the action - its purpose is relief. Once the relief is set I like to do the nut slots but I approach the final settings slowly. I use measurements (somewhere around 0.014 on the high E to maybe 0.018 on the low) but I also want to be sure that as I fret at the 3rd fret there is clearance at the first. Go slowly, its hard to make the slot less deep.
Next is the action over the fretboard - usually measured at the 12th fret. Again, you will find all kinds of numbers measure yours, lower it a little, see how it feels. For many guitars I find that somewhere around 0.060 on the high E and 0.090 on the low, with each string in between getting a little higher, works pretty well. Last I check the intonation of each string - play the 12th fret harmonic (which should be one octave higher than the open string), fret it at 12 and compare the note. You can do it by ear but I prefer a good tuner. If the fretted note is sharp, move the saddle away from the nut a bit, check again. Adjusting the intonation should not affect the other setup parameters, changing some of them may affect intonation.
Now just play every fret on every string listening for any buzzes or other nasty sounds. See if the action feels right to you up and down the f/b - if not try to figure out why. At this point I go back to the spreadsheet and write down everything once again, date it and put it in the case with the guitar - the owner has a very good record of what was done and how the guitar was returned.
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