I am going to go against the grain here, but you can try the 650 carbs in the 550 and probably get it to run okay. I have both bikes and my 550 didn't run well with the stock setup. Pretty sure it was nearly stock with aftermarket main jets. Since I had an extra set of 650e carbs sitting on shelf, I decided to play around. First was replacing 650 carbs with 550 parts. Ran about the same, still pretty long warm up needed, excessive bogging until fully warmed. Then I went the other direction with 650e bits. No longer required the 2 minute warm up and seems to give a little more total zip. I haven't ran it more than about 15 minutes, but still doesn't run nearly as nice as my 650g at all speeds.
I will tell you that the 550 carb parts; needles, slide springs, are much different from 650s. The 650 shaft drive models also seems to be tuned a lot richer than 650 chain drive on main jets (110 vs 97.5). Conversely the main jets between 550 and 650e is similar 92.5 vs 97.5.
I find these changes interesting since there is only a 123cc difference in motor displacement.
One thing you may not consider with the carb body swap is that there are non replaceable air jets that are different between models. Likewise, the throttle butterflies are numbered different.
Here is compiled data from top link of tech section
GS 650 GZ/GLZ (82)
idle r/min 1100-+/-100r/min
carb mik bs32ss (4 seprate carbs)
id no 34300
bore size 32 (1.26)
float height 22.4.+/-1.0 (0.88 +/-0.04)
fuel level 5.0+/-0.5 (0.20 +/-0.04)
main jet #110
main air jet 2.0
jet needle 5C45
needle jet Y-7
pilot jet #42.5
throttle valve #135
by pass 0.8, 0.7, 0.8
pilot outlet 0.7
valve seat 2.0
starter jet #45
pilot screw pre-set (1.5 turns back (mixture screw))
pilot air jet #160
throttle cable play 0.5-1.0 (0.02-0.04)
choke cable play 0.5-1.0 (0.02-0.04)
GS550 (80-82) the specs are for the CV's
idle r/min 1100-+/-100r/min
carb mik bs32ss (4 seprate carbs)
id no 47160 (us) 47170 (can)
bore size 32 (1.26)
float height 22.4.+/-1.0 (0.88 +/-0.04)
fuel level 5.0+/-0.5 (0.20 +/-0.04)
main jet #92.5
main air jet 1.6
jet needle (4bel2 us model) (5f42-3rd notch canadian adjusable needle)
needle jet x-6
pilot jet #40
throttle valve #135
by pass (0.9, 0.7, 0.7 us model) (1.0,0.8,0.8 canadian)
pilot outlet 0.7
valve seat 2.0
starter jet #35
pilot screw 3.5 turns back (mixture screw)
pilot air jet (us model #150) (#120 canadian)
I can't copy 650e info, this link has it;
http://www.thegsresources.com/_forum/showthread.php?t=73723&page=5
Clean them up and give them a go, I would bet it won't run that badly.