I have an 79 XS400. The motor ran pretty good the last year or so. I noticed that it was only running on one cylinder at idle the other week. I adjusted the carb blance until both ran. I also set the pilot air screws to the stock setting of 1-1/4 or so turns out. I noticed some weird things getting worse now... The bike idles bad and if I turn the choke on it trys to shoot up to 5,000 rpm. The left side exhaust also likes to pop... It takes longer than normal to return to idle after reving the motor. Driving at half throttle or more feels normal although I can feel a slight on and off surge of power... when I come to a stop sign the motor stays at 3500rpm if I turn the idle adjust screw even a bit it drops down to 1500 or stalls. Everything points to a air leak but I can't find any. I used some starting fluid and checked for air leaks.. found nothing (not very safe, but I wanted to make sure)
This problem got really bad after I removed the factory caps on the air screws. How picky are the carbs? Would being out of blance by only a 1/8th turn cause the whole thing to run this bad?
My other question is, can the problems i'm having be caused by leaking slide diaphragms? They look to be fine and slide free and work when tested by blowing air into the carb. The bike runs fine at high speeds.
I really don't want to spend 50 bucks on a pair of carb kits only to find out I need the only parts that cost more than the bike (the slide/daphragms) I would rather spend the money on a set of new modern slide carbs instead of more parts for old ones.
Things I have already done/checked
Carbs broken down and rebuilt. dipped and blown out with compressed air. Float hights set.
Tried to blance the carbs.. nothing seems to make it happy.
Valves adjusted
Compression checked with gauge
Replaced points, set timing.
Fresh tank of 93 octane.
XS400 Random idle, stalling, spitting
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BuzZz
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It sounds as if the idle circuit is too lean now with stock settings. Turn the ilde air screws richer and see if that helps. Best to go a quarter turn at a time and test run it each time, rather than cranking them 2-3 turns at a time. It might be a bit more tedious, but it's less likely to hurt something by going too far at once.
No Witnesses.... 
You know.. I think I got it dailed in. 
Trying to blance carbs based off the sound of the motor is very hard in general..even more so if you messed with air screws. On a small twin motor it's not always easy to tell if its running off both clylinders or if you are cranking one setting too high, allowing one clylinder to do all the work. It would sound like it was running good.... then pulling the choke would allow the other cylinder to kick in and rev way up.
I have a pretty good tip for everyone trying to blance carbs on the fly.. Set the blance as close as you can with the carbs off, then warm the bike up and leave the choke half open.. I found the motor always ran on both cylinders with the choke half open and this allowed me to switch between no choke and choke until I got everything set. When trying to blance the carbs with the choke off, I would always run into a problem where the motor would rev way too high (above 5k) with the choke open. Setting them with the choke on allowed me to have a 2500 rpm choke and 1500 off choke idle.
Trying to blance carbs based off the sound of the motor is very hard in general..even more so if you messed with air screws. On a small twin motor it's not always easy to tell if its running off both clylinders or if you are cranking one setting too high, allowing one clylinder to do all the work. It would sound like it was running good.... then pulling the choke would allow the other cylinder to kick in and rev way up. I have a pretty good tip for everyone trying to blance carbs on the fly.. Set the blance as close as you can with the carbs off, then warm the bike up and leave the choke half open.. I found the motor always ran on both cylinders with the choke half open and this allowed me to switch between no choke and choke until I got everything set. When trying to blance the carbs with the choke off, I would always run into a problem where the motor would rev way too high (above 5k) with the choke open. Setting them with the choke on allowed me to have a 2500 rpm choke and 1500 off choke idle.