Congrats on your Ric!
To address some of your concerns:
Problem One: Don't know what to say about that one, unless you can just get a rag and try to get a really good grip on each nut and kind of "rock" the threads free. A small amount of WD on a toothpick and a slight tap on the knobs with a mallet might be helpful. If you want a new rubber pad, they are pretty cheap.
Also, consider a Hipshot bridge if you don't need the mute. Intonation adjustment is 100 times easier, and no "tail lift!"
Problem 2: Weak E string is a common problem. First thing to do is to try a new E string, just in case the one on the bass has gone bad. If that doesn't fix it, experiment with pickup height on that side. Closer isn't always better. Also, make sure that the E string fits well in the nut. The Ric was originally kitted with lighter strings, and if someone strung it with a .105 or .110 or something, it might be binding in the nut. Also, check the saddle to see that the string fits nicely in the groove.
Concern 1: There shouldn't be much relief at all. The neck on a Ric should pretty near flat, unlike most other basses. The truss rods being adjusted "unevenly" is OK, as long as there are still threads left.
One BIG warning... the 4001 needs to have its truss rods adjusted (tightened) in a particular way, or you risk popping the fretboard off! The 4001 needs to have its neck more or less bent to the desired position and held there while snugging down the rods. The 4003s had the system redesigned, and one doesn't have to worry about that anymore.
As far as setup, if you get the neck more or less flat, it's just a matter of lowering the action until buzzing occurs, and then backing off slightly. You can get really low action on a Ric, though high action sounds great, too - just tweak the pickup heights a little.
The Ric site (
www.rickenbacker.com) has a very useful forum full of very knowledgeable folks. I'm sure they could answer your questions much more thoroughly than I was able.
