I've been following this for a bit to see where it's going and thought I'd jump in. My bike is a '79 GS1000N and at one time had a factory "S" fairing, brackets, mirrors, etc. '79 "S" was merely cosmetic so it should be equivalent to yours. Right now it hasn't got the fairing anymore (I broke it) but with or without it the handling didn't change. My setup is progressive springs up front w/no air and 15W fork oil and STOCK rear shocks set usually on the stiffest setting and damping set at max. I quite often push the handling capabities of my bike to the extreme and other than the occasional wobble or weave (a fork brace fixed some of that) it handles just fine. Maybe this can be used as a baseline to get yours sorted. I think as long is the stock shocks haven't developed any leaks they should work fine. The stock front springs are known to be downright awful though.
The front and rear wobble and weave are coupled and it is difficult for most mortals to soth out the cause and effects, so I think what I'm finding out is when all else fails measure the sag first and go from there.