I changed my fuel/jetting back to "stock" recently, and things are working OK, except for an occaisional bogging while releasing the clutch, at low RPM.  Right after an up-shift, when rolling on the throttle and releasing the clutch, the bike acts like it's in too high a gear, chugging and lurching, until RPMs reach about 3.5k.  At about that point, the engine smoothes-out and behaves like it's supposed to.

The problem seems to come and go.  Last week, my ride to work (10 miles freeway, 4 miles city streets) was fine.  After a few freeway miles on the way home, the problem happened, and I thought the bike was maybe missing on one cylinder or something.  I got off the freeway, and the whole way home was chug-shudder-chug, every stop sign and stop light.

Today, the ride to work was fine, but then when I left work (cold bike), I experienced the problem again, so I kept the revvs higher (upshifting from 6k to 4k).  I was also riding about 70mph.  Once I got off the freeway, things seemed fine: no stutter or loss of power when upshifting from 5k to 3k; no need to rev higher to avoid a stutter.  Whatever the problem was was gone.

You returned jetting to stock.

Did you also return air filter/exhaust to stock?

What year is your GS? (Or at least what year are the carbs from - 2-circuit .vs. 3-circuit)

My first guess is fiddle with the pilot (idle) mixture screws - perhaps those are not set right?

It's a '92.  I put back the paper filter, stock exhaust, 40 pilots, 122.5 mains, no needle shim, idle adjust screws 3 turns out each.

It seems to idle fine.  But you're right, I could play with the idle screws. In past years, I mostly noticed they needed setting if the bike was killing when coming to a stop.  Right now, I have no issues with idle if I pull the clutch lever... only under load, at low RPM.  The weird thing is that it comes and goes.   

Intermittent vacuum leak? Cracked hose or intake boot?