2004 Honda CB599 cylinders 1 and 2 don't run

Question

Hello I appreciate any input you might have.

This all started yesterday, I have a 2004 Honda CB599 carbureted.
I was using a little tire pump to put air in the tires and the bike suddenly died. I figured the idle was too low or it was too much for the old battery. I took the battery to be tested (it failed) and got a new one. I also adjusted the idle using the idle screw (also knocked off a vacuum tube and didn't notice).

I proceeded to flood the engine because I didn't notice the disconnected tube.

I pulled the plugs and fixed the disconnected tube. I cleaned and dried the plugs while I cleared the engine of gas (ran the starter a couple of times with the plugs out)

I tested the plugs, blue spark on all plugs. And reinstalled everything. The bike only runs on cylinders 3 and 4. I'm not sure what I'm missing or what I should check, but I am out of ideas and could use some advice.

Thanks in advance.

Pav_S · Answer

[FIXED] 
I cleared the engine again by running it without the plugs in. Dried the plugs and drained all of the gas out of the carbs (screw on the bottom of the carb above the drain nipple).

I then reset the idle screw to two turns out and reinstalled the plugs.

I ran the starter with the gas off and to my surprise it started right up. I quickly turned the gas back on and let the bike warm up.

I then adjusted the idle screw to (1400+-100 RPM)

The previous owner installed a high flow air filter and a two brothers can. I think the carbs need tuned and I've been looking for a comprehensive guide on how to do it myself.

2004 Honda CB599 cylinders 1 and 2 don't run

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