Wes, I am assuming your are building from some sort of plans that has a profile (side) view of the neck angle, pickups and bridge. If not you should draw your own because the angle is a function of a bunch of things that will vary from guitar to guitar. First, most LP Jr's have a flat top (no arching) and the fretboard stands proud of the body by some amount. From there draw a line that represents the frets extended to bridge. Now draw the normal playing action you want, lets say 0.060 to 0.080 at the 12th fret) and extend that to the bridge. That is about where your ToM saddles will end up (there will be a small effect from the relief in your neck). You want your neck angle such that your ToM adjustment allows you to go up and down a bit from the playing action.
I've had very good luck setting the neck so the fret plane is as low as the ToM can go - to test that I put the bridge on a couple of pieces of wood that are the thickness of the studs
The fretboard is fretted but has no relief.
I have scanned my Les Paul plans and could send you PDF's of the neck to top profile. It is fairly easy to measure the height that the fret plane should be over the top, but remember that this is a carved arched top. Might get you started at least.
Last comment, as far as locating the bridge relative to the end of the fretboard (scale length) I have found the StewMac fret board calculator to be helpful. After running the calculations they have a drop down for you to select the bridge you plan to use - it will give you the compensated location which seems to work pretty well (as far as putting the adjustment in the middle of the range).