It isn't so much about the pods regarding syncing. You want to get the vacuum equal across the four carbs so each cylinder is working equally, this makes the idle as even as possible. With unbalanced carbs the idle is always lumpy since one cylinder will be firing stronger.
In your situation I don't know what the carb tuning has been. Was it ever set up for the pods and you're fine tuning, or did you put them on and are starting from scratch?
Usually pods require a pilot jet one size smaller than stock. The idle and low throttle mixture will be messy without this change if it's needed.
Before doing carbs you must have the ignition timing and valve lash set correctly.
Try to get the carbs synced as close as possible at as low a stable idle as you can get. Don't adjust all four carbs if all are adjustable, I think the 550 has #2 as master and non-adjustable but some racks have all four adjustable. If you adjust all four you screw up the idle, wide open limit, and choke throttle advance settings. Once you have the sync close it may idle better.
Next do plug chops at wide open throttle and RPM in the upper third of the range, this usually means finding a quiet highway. You need to get the correct main jet first. You may be able to get a jet kit with assorted sizes from siriusonline.com or you can guess and get them from Honda. If you're starting from scratch with pods and the plugs look grey go up 4 numbers at first, this should be close. No guarantee.
Next (once you have mains that show a nice brown on chop) try a chop at 3/4 throttle (mark a scale next to the twist grip) and 1/2 throttle. You look at the progression basically. If plugs are browner at 3/4 and blackish at 1/2, you need to drop the needles at least one notch. You may be cursed with one-groove needles, hope not. If they are lighter brown at 3/4 and greyish at 1/2, raise the needles a notch. Repeat until you get brown plugs. Lowering the needle means putting the clip in a groove closer to the blunt end. Naturally you get to re-sync after pulling the needles.
Last you look at 1/4 throttle, probably this will look rich and you need that smaller pilot jet. If it's OK, and you have the sync close, set the screws. Start from the stock setting from your manual and without chaging your idle setting, screw all four out 1/4 turn. If the idle speeds up, screw them 1/4 turn more. repeat until the idle starts to drop and go back to the previous setting. If the idle drops at first, screw them in for the same effect.
Now check sync again. You should be able to set a 1200 RPM idle or so and set the sync to get it purring.
Any problems probably relate to dirty carbs, you have to be really anal about cleaning the things. Make sure the emulsion tubes have clear cross holes especially, the pilot jet should have one attached and the main jet has a separate one "above" it, the needle slides through a hole in the top of the emulsion tube. It should press down and drop out the main jet hole easily with a little push from the bore side.
There are some theories about modifying the emulsion tube by enlarging some of the cross holes, but if you can get the bike running OK without that I think you're good. Clean these tiny cross holes with a soft copper strand from an stranded wire (like the harness wire), not anything harder than the brass they are made of.
