I had my 82' L2000 in storage for a couple of years, with the strings at half-tension. The neck doesn't look warped, but I still get string buzz at the third fret, even with the bridge saddles nearly maxed out in height. It doesn't buzz in the upper registers, and in fact the action is way too high for my taste just to get rid of the buzz, giving me a lot of "clank" as the string bangs down against the frets as I finger it. The intonation is near perfect, but the high action is really annoying me. I tried tightening the truss rod to reduce neck relief, two 1/4 turns. Am I going the wrong way? Should I loosen the truss rod to increase relief?

if the buzzing is down at the nut end then I'd guess the nut may need a little shim under it to raise the action there a bit. Once the nut is higher then you can tighten the truss rod a touch and get the strings closer to the frets up at the high end, and generally improve the overall action. Good action at the first three frets - you should be just able to shove a 0.7 - 0.8mm pick in between the high string and the fret and get it to hold.
At the 17th fret the action should be about 1.0 - 1.5mm on your G and 1.5 - 2mm on your E.

Buzzing at the third fret is not the nut. Sounds like your neck needs relief. In the setup area there's some stickies up top.

If your strings buzz down low only => too little relief, loosen rod

If your strings buzz up high only => too much relief, tighten rod

If a given string buzzes everywhere => raise saddle.

Since you left your bass deturned, the neck could get some memory of that position and need to have the truss rod loosened. Hopefully that will fix it. You do not want to leave a neck in an unnatural shape for extended periods of time.

Thanks Guys,
I tried loosening the truss rod back off the 2 1/4 turns i cranked it up, plus another quarter turn looser. The 3rd fret buzz disapeared immediately! Thanks for the help. Damn I love this bass. I can't remember why I ever put it down.

Be careful. I just caught that you did 2 1/4 turns at the start. That is a lot. 1/4 turn at time. After a 1/2 turn or so, give the bass a day or two to settle.

BTW you can measure relief with a capo and a set of feeler gauges. Both can be had for less than $5 if you do not own them. I also measure even if I have it set differently on different basses. And when I get a good setup, I record the measurements. This can be helpful if you experiment a lot with different strings.