Back firing and doesn't fire on on cylinder until warm

Are you certain it is still getting fire once warmed up? Sounds like you might have a bad ignition module.

4 cylinder engines can have both firing orders
the more common one is 1-3-4-2 but some manufacturers have the other firing order
it depends on the manufacture of the position of the crank pin
some reason for it are
less harmonic vibrations
less stress on crank webs
easier manufacturer
for the missing problem run the fault codes and check for ambient temp sensor , maf/vaf sensor or BARO sensor problem

Carburation! If the air/ fuel mixture is not carefully adjusted by the choke system after warmup it will do just what you describe...check it out!

You put something back the wrong way.....any amount of water in the tank, carb or whatever WILL NOT cause the engine not to fire.....check any wiring/rewiring you did for accuracy

You have to test all the electronics on the bike to figure out if you have a bad CDI box. A CDI box can test good and still be bad. Your problem sounds more like a bad spark plug cap. Unscrew the cap from the end of the wire and take an OHM reading on the cap. If it is higher or lower than 5000 OHMs replace the cap . A plug cap from NGK runs about $5. Replace them both for about $10 it should take care of the problem.

check map sensor, It sounds like its failing

ok buddy on number one cylinder carb will be a screw on the carb fiddle with this screw till it runs ok the mixture screw get back to me if not ok

CHECK THE SPARK PLUG +WIRE +COIL.TO THAT CYLINDER.IF ALL IS GOOD.DO A COMPRESSION TEST ON THAT CYLINDER. IT COULD BE MECHANICAL PROBLEM IN THAT CYLINDER.LEAKING VALVE OR INTAKE LEAK.

Have you done a compression test on it. Try that. It also could be a valve, electrical or fuel problem.

if the coolant temp sensor is faulty it could be causing a fuel problem or maybe a fuel pump