What Andy said. The truss rod should only be used to set the relief in the neck with the strings at normal tension. Though it does play a part in the overall action you get, it's the first thing to set up and after that you can normally forget about it. After that it's setting the bridge height, then the nut slot depth and then the intonation (saddle position).
It may be that some of the frets are higher then the others, but take things one step at a time. A notched edge has cut-outs for the frets, so that you can gauge the straightness of the fingerboard itself, without having to take into consideration any high (or low) frets. It's not 100% necessary to have one, but if you want to build or work on more guitars in the future, then its a great investment.
The neck should be slightly concave, just off flat. Hold the top and bottom E strings down in turn at the first and last frets, and you should just about be able to see a gap between the tops of the 7th and 8th frets and the string. The size of the gap can come down to personal preference, but around 0.5mm should be sufficient. Much above 1mm and there's a bigger gap than necessary, which will give you a higher overall action.
The next step is to adjust the bridge height. Always adjust it with the strings slackened, but always test it with the strings at normal pitch. You need to adjust it so that you lower it as much as you can and still have all the strings playing cleanly, without any buzz. You haven't done anything with the nut at this point, so the overall action will probably come down when you do, but you should be able to achieve a gap between string and 12th fret of around 1.0-1.5mm on the top E and 2.0-2.5mm on the bottom E.
If the gap has to be much larger than this, then there is probably an issue with one or two proud frets. You should be able to check by lowering the bridge height a bit until you get most of the frets sounding cleanly, but there are one or two places where the strings buzz against the next fret (or two) up.
If the strings are buzzing on the first one or two frets, then the nut slots for those strings are probably cut too low.
This is where the notched edge and the Stanley blade rockers come in, as you really need to confirm which frets are causing the problem.
But get this far and get back to us with measurements and/or photos if there are any of the issues listed above.