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Are the plug leads in the right order could 1 & 2 be back to front?
One coil only runs cylinders 1 & 4 with the other coil running the 2 & 3 pair.Easy to quick check, no numbers needed.Another easy test, if you've any e-z-start or brake cleaner, you can put a little squirt into the cylinder via it's sync port while its running to see if that pot will chime in, obviously then indicates fuel absent on that one.
The other possibility if ht leads are correct is kinked fuel pipe to 1&2 or a blocked tap outlet to 1&4
Your remarks are contradictory. You say the floatbowls fill up and you don't rule out you've kinked lines.If you're unsure, I'd begin by tapping (gently) the floatbowls with the stub end of a screwdriver to activate sticking float needles and/or remove dirt in between the floatvalves and their needles. Often this is all what it takes.If you're sure the floatbowls do fill up, this is what I'd do.Do a start attempt and then check the #1 and #2 sparkplugs. If the plugs noses are dry, fuel does not arrive. If the plug noses are wet, fuel does arrive and the problem is elsewhere.If the fuel does not arrive, I'd leave the carbs where they are.Unscrew the airscrews from the sides of the affected carbs (after writing down the position they were in) and spray carb cleaner using a straw in the openings and hope it will clean the slow jets. Reposition the airscrews and start engine. Maybe the carb cleaner has cleared the slow jets. I had success with this once.If not. On a CB550 LH side I find it not difficult to just unscrew the floatbowls with the carbs in situ and then remove their jets for inspection. Long time ago I have replaced the 4 crossheads of every floatbowl by allen. Much easier. All maintenance/cleaning on these oldstyle carbs can be done with carbs in situ. It helps if you're familiar with what's inside though.
The tube to the T-joint 1+2 should be 17 or 18cm long, depending of the model petcock your Cb550 has. The oldstyle petcock with the bowl requires a length of 18cm, the newer type 17cm. Ideal ID is 5,5mm. After a long period of sitting you can expect irregularities. When carbs have been drained for a long period, O-rings at the T-joints will shrink and so - possibly - cause initial leaking. Usually the rubbers will regain their original dimensions, but I prefer to keep my carbs in a natural state, which is wet. As far as problems with the floats, both valves and needles, tapping (gently!) the floatbowls with the stub end of a screwdriver can do miracles. Flushing the floatchambers by removing the drainscrews and then opening and closing the petcock can also help, or both methods combined. Make sure the joined vent tube for carbs #1 and #2 is free and can vent to the open.