The bike runs as good as ever when I start it, but as soon as it gets warm and i try to ride it, it only runs on one cylinder.
And even worse is that after only a couple of 100 meters it starts to fail on the other cylinder too, making it impossible to rev it up and finally it will just stop.
If I wait a couple of minutes it will start again, often running on only one cylinder and it will die as soon as I try to drive away, but sometimes it will run on both and i can drive avay a couple of 100 meters until it fails again.

Anyone have a clue what could be wrong?

I have three possible things in mind, either the carbs need a clean up (but not likely since they were cleaned last year, and the bike have been standing still for over 6 months) or the sparkplugs need to be changed (but that's not likely either because they were changed the same time the carbs were cleaned.) And the last thing I can think of is that the PGM-II is faulty in some way, making the bike not ignite...

So could it be one of those reasons? Or do you guys think there could be another reason?

Thanks

If that were my bike, I'd be thinking fuel starvation. Have you checked the flow from the tank to the carbs ?

Try running it with the petrol cap open, if the tank breather is blocked or restricted, you'd gradually create a vacuum in the tank, restricting fuel flow...

Start with, and eliminate, the simple things...

the usual suspects are cracked inlet manifold, crank seals, spark plugs (even if they are new), crank case seal, cylinder base gaskets, dirty petrol, as its a 18 what state is the battry charge wise, clean the carb again.
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Honda nc23 CBR400 AERO 1986, 1990 honda NC23 Tri-Arm, 1987VFR400 NC24 Rothmans Rep, NSR250 MC16 1987, CL250s 1983. Moto guzzi zigolo 110cc 1958. Fantic 50cc 1972. Suzuki Cobra Race bike 500cc 2t 1975 , GP125 1975. Triumph T110 1954. BSA Thunderbird 1955. Ariel VB 600 1952, 1990 MuZ 125 etz.

If you find that the fuelling is fine then check your coil connections. you're looking to see if there's any scortching etc. If so then it's a bad connection and breaks down when hot. Easy fix is pop a new connector on the harness and make sure it's a snug fit. Check and clean all other connections while you're at it.

Seen this a few times, but I'm not saying that's your problem.

I had a similar problem with my 18 ,it would run in the garage fine but would cut out 1/2 a mile down the road .I'd push it back strip it down but was unable to find anything then a couple of hours later it would start first kick and the game would start again. Anyway what it was, was a frayed cable at the pick up at the rotor which when it got warm and with a bit of vibration would short out and the PGM would kind of shut down. This was found after replacing the PGM and most of the multipin plugs with bullet connectors. It may be worth a good look.