Brian, do not worry about the vertical component of the rear at this time. Aligning the rear is a horizontal measurment. The rockers are the key. Take a vertical line on the tire and measure the distance from the end of the rocker to that line. Both sides have to match. it is not that important on how you measure, but that you measure both sides from the same points. If they are equal, then the rear is aligned with the body. (centered in the wheelwell and height above body is a whole other story!)
Next on the the front, caster is how much the vertical axis of the spindle is leaning fore or aft. That is not easy to do without the proper tools, so lets leave that for now. http://en.wikipedia.org/wiki/Caster_angle
Camber and toe can be done. Camber is the the lean of the spindle in and out http://en.wikipedia.org/wiki/Camber_angle
for a rough alignment, you want the tire vertical. Just place a piece of wood that matches the dia of the rim, place on the wheel and take a level to it vertically. If the top of the wheel is closer to the engine, add equal number of shims to each of the bolts on the upper A-arm. Wheel top out more than bottom, reduce shims.
Toe, get a peice of straight wood about 6-8 ft long, then get 2 2x4x4 peices and attach them to the long one so the small pieces can touch the tires on each side. Then find another person and a flat section of pavement. drive car as straight as you can and park. Then place the wood on the tire facing foward, have other person mark the pavement at end of wood, then flip and make a mark in the back. Do other side same way. Measure the distance between the front marks and the rear marks. If front is wider than rear, you have toe out. fix by lengthening each tie rod. If front is narrower than rears, you have toe-in, which is what you want.
You can also measure the body against the marks to see if your wheels are straight with the body and then use that to adjust the tie rods in opposition. That is how my dad did his on the cheap