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GS550T running lean, what else to check?

Just read through all of this and noticed a couple of points.

If there is no difference between 0 turns and 3 turns on the pilot screws, it sounds like there is nothing coming through the pilot passages. Your JET might be clean, but I don't think that PineSol is a proper solution to remove INTERNAL carb deposits in very small passages. By the way, how long was the PineSol solution in contact with the carbs?

Manifold boots should be almost as pliable as a diver's wet suit. Almost. Yeah, they can be softened a bit with wintergreen oil, but that does not fix the real problem. The only real fix is to bite the bullet and get new boots.

Valve clearances will affect the ease of starting and basic cold operation. Depending on how tight those three valves are, they should be adjusted.

Idle speed should be controlled at the carbs, not the throttle grip. Even when set properly at the carbs, if the cable is just a little too tight, idle speed will change when the handlebars are turned. There should be enough play in the cable to allow moving the bars fully lock-to-lock without changing idle speed.

Yeah, new boots might be $120 (actually, I just checked, saw them for $135), but how much fustration are you going through while denying that they might be the problem? I have worked on a couple of 550s and know that they are tight. You say you have large hands, which only compounds the problem (my hands aren't exactly 'petite', either). I would HAPPILY pay someone $120 to work on a 550 to do something that I am well-qualified to do, just to avoid going in there again. To have the luxury of spending a bit of money to fix the problem and be done all of a sudden seems to be worth it.

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Lots of info to digest. some quick responses after pulling the carbs off this morning ...
1. The pinesol bath was a 50/50 mix in an ultrasonic. Carbs were in there for ~10 minutes followed by compressed air through all passages. I don't leave carbs in the bath in too long since PS can eat away at the metal. I've used this process on many other carbs and it works well.
2. the intake boots are not anywhere near a wetsuit. Biting bullet on new intake boots and other supplies today
3. Part of the supplies in #2 will be a valve cover gasket, so I'll resolve the valve clearances while I have everything apart. The tight valves are not touching, the shims&buckets still spin freely when in checking position, so maybe they are .01+ mm
4. I was adjusting the idle via the throttle cable control as a short term method since it's easier to reach than the idle screw, which I've now learned is better accessed from the right side of the bike than the left. In hindsight, the butterflies had been left slightly open (less than 1mm visual), which should not be enough to cause 4-6k rpm surge.
5. The carb-airbox boot on carb2 was not firmly clamped to carb2. It fully covered the throttle opening but the light clamp pressure probably allowed some air. Hard to say if it was the sole cause of the surge.
6. In general, the carb-airbox boots are intact, but the rubber has probably shrunken over the years since they can rotate in the airbox openings. Some silicon sealant might help.
7. As mentioned, i'll be getting the new boots. This is a cheap bike that I bought as a non-running project, so I didn't want to spend a lot up front until I had at least heard the engine run. Now that I know it's not DOA I'll be more willing to spend ... within reason.
 
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If the boots are properly fitting you won’t need any sealant. As Steve suggested, get new boots for both sides of the carbs; you’ll be amazed at how much faster the carbs jump into their location too
 
If the boots are properly fitting you won?t need any sealant. As Steve suggested, get new boots for both sides of the carbs; you?ll be amazed at how much faster the carbs jump into their location too
The carb-airbox boots are available for cyl1&4 (13882-47030), but not 2&3 (13881-47030), at least not from partzilla. I'll look for other sources, but avoid BikeBandit who has gotten really slow lately.
 
Regarding your point #3: don't rely on the fact that the bucket will spin to say that there is clearance. I opened up one engine that was new to me, so I could check clearances. Found one that would not allow my 0.0015" feeler. The bucket would spin, so I went one size smaller on the shim. Still would not allow my thinnest feeler. Went down another shim, STILL would not allow my feeler. Ended up dropping three shim sizes before I had measureable clearance.
By the way, this would be a good time to make you aware of the offer in my signature.

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Check out PartsOutlaw.com; I just picked up new boots for my daughter's 81 550L a few months ago without any issues
 
Regarding your point #3: don't rely on the fact that the bucket will spin to say that there is clearance. I opened up one engine that was new to me, so I could check clearances. Found one that would not allow my 0.0015" feeler. The bucket would spin, so I went one size smaller on the shim. Still would not allow my thinnest feeler. Went down another shim, STILL would not allow my feeler. Ended up dropping three shim sizes before I had measureable clearance.
By the way, this would be a good time to make you aware of the offer in my signature.

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Thanks. I've done valve adjustments on other Suzuki GS450's, so hopefully I have shims on hand that will meet spec.

I'm still debating if I only check&adjust clearances, using the bucket depress tool to access the shim, or go big and pull the cyl head off so that I can change the valve seals and generally clean things up. THis would mean re-setting the timing chain and camshaft position, which can get tricky. It's winter, so I have time, and I have other bikes to ride should a good day come up.
 
Other than the few times the engine has started (as reported in this thread), have you ridden the bike at all? :-k

Replacing valve seals can be a worthy task, but if the bike is not smoking or burning oil, I would not bother with it.

Adjusting the valves is a little different between the 450 and 550. On the 450 (and other twins) you simply place the cam lobe opposite the valve. On the 550 (and other fours) you have to pay attention to the adjacent lobe and place both of them so neither one is pushing on a valve, then check BOTH valves.

If you do pull the head, resetting cam timing isn't all that bad. Installing the tensioner is the hardest part, but is actually rather easy. It's also easy to do it wrong, but following the instructions works quite well.

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Other than the few times the engine has started (as reported in this thread), have you ridden the bike at all? :-k

Replacing valve seals can be a worthy task, but if the bike is not smoking or burning oil, I would not bother with it.
<snip>
If you do pull the head, resetting cam timing isn't all that bad. Installing the tensioner is the hardest part, but is actually rather easy. It's also easy to do it wrong, but following the instructions works quite well.

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The bike is new to me and being resurrected after the typical neglect. The test starts mentioned in the thread are the only experience I have with the bike.

Besides the first few test starts I did not see any abnormal smoke, so it sounds like your recommendation would be to leave the head in place and just to the normal valve adjustments.

If I choose to go the long route, I have pulled the head on one of the 450's I've owned previously including removing the valves and resetting the cam chain tensioner, so this would not be new territory. Snowing today in New England, so it looks like a long winter.
 
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