Also, do this at "your own risk", and "I take no responsability" if you screw your guitar up, and I am "NOT" a certified guitar tech.
Neck Relief
The neck relief effects the action but should not be used as an action adjustment. Rickenbacker recommends the neck to be set just about dead flat. The dual truss rod allows you to adjust the base and trebble side of the neck. This is a great idea, but be carefull with it. I'm not saying to be affraid of it, just be careful not to put too much tension on one side compared to the other.
What I did when I first got the guitar was to loosten both rods all the way and then turn both rods the exact same amount at a time until the neck was just about dead flat. The reason I did this was because for all I know the idiots at Sam Ash could have been messing with these adjustments, and I just wanted to be 100% certain that there was the same amount of tensions on both sides of the neck.
One good way to adjust your neck relief is to put a capo on the 1st fret, hold all the strings down on the last fret, and check for a gap between the strings and the frets about the 8th or 9th fret. Do this with the guitar tuned to pitch and check all the strings. They should be just about touching the frets. If one side (base/trebble) has a little more of a gap than the other, adjust that side just a little bit more (no more than 1/4 turn) and give the neck time to settle (a few days to a week). I wouldn't put too much more pressure on one side compared to the other, because over time, you could wind up with problems.
Nut Action
I recommend setting your neck relief before adjusting the nut action. If you have a lot of neck relief, and adjust your nut action first, and then set your neck flat, it could change your nut action enough to cause buzzing on the open strings.
If you have a set of nut files, you can leave the guitar tuned to pitch and adjust each string one at a time. Fret the string at the 3rd fret and press down the same string at the 1st fret. There should be a very slight gap between the string and the first fret. If there is too much gap, pull the string out of the slot (carefully) and move it to a spot that it will stay at. Gently run the nut file through the slot and take off a little bit at a time. Put the string back in the slot and check it each time until all the strings are to your liking. The strings should not buzz open with even hard strumming, and first position bar chords should be easy to play.
If you do not have files small enough, you can adjust your nut action from the bottom. Rickenbacker does a great job of making their nuts to follow the fret radius, so rubbing the nut accross a piece of sandpaper evenly at the bottom, you can get a good even nut action as well. This requires loosening all the strings, removing the nut, sanding a little at a time off, replacing the nut, and tuning back to pitch to check it each time. If you do it this way make sure you sand it square and flat at the bottom so it fits nice and square.
The nut should pop right off with a little pressure, and you should be able to shave the glue off with a razor. Do this very carefully. A couple small drops of elmers wood glue works good to put the nut back on, and gives you plenty of time to position the nut before drying. The string tension will hold the nut in place while the glue dries. Only use a very little amount of glue because you wanna be able to pop the nut back off if you need to.
Action
Now that you set your neck relief and nut action, you can set your action. Remember when I said that neck relief effects your action but should not be used as an action adjustment? Well, if you set your action first and then set your neck relief, you will find yourself setting your action again. Right?
The action is adjusted using the four screws on each corner of the bridge assembly. Make sure the bridge sits square with the bridge plate, and all four screws have equal tension. I think Rickenbacker recommends 5/64th's base side and 3/64th's trebble side. Check the action at the 12th fret and measure between the top of the fret and the bottom of the string.
Check every string at every fret for buzzing and adjust the action acourdingly. Once you eliminate any buzzing, play the guitar and tweak until it feels right to you.
I put a set of D'Adderio Chromes 12's on mine and was able to get the action to 3/64th's on both base and trebble sides without any buzzing. It's actually easier to play than it is with the 10's on it...
Intonation
Since my guitar has 24 frets, I check my intonation with a tuner at the 12th and 24th fret. If there is a difference between the 12th and 24th fret, I find a happy medium between the two.
If it is sharp, adjust the saddle closer to the tailpiece, and if it's flat, andjust the saddle closer to the neck. Hold the string off of the saddle while adjusting to relieve drag caused by the string tension.
Pickups
This is a matter of taste and is very subjective, but I found a good starting point for pickup height which works well for me.
Adjust the pickups to 1/16th from the top of the pole piece to the bottom of the string on both the base and trebble side on both pickups. Do this with the strings held down at the last fret and make sure the pole pieces for the base and trebble strings are screwed in all the way. If you want the pole pieces to follow the fret radius, adjust each pole piece to 1/16th from the top of the pole piece to the bottom of the string while holding that string down at the last fret. You can also choose to just set all your pole pices all the way in as well. This gives a very good sound as well.
This seems to be a good starting point for me, and you can adjust them any way you want depending on the tone you are seeking...
In Closing
Setup is very subjective, and this is only a starting point in which to go by in setting up your beautiful Rickenbacker.
Experiment and have fun, but most of all, play it...
Peace