Possible root causes for engine that over heated

I apologize in advance for the long post, but lemme give you some background:

Last October, I had to ride my KZ750 LTD to work while it was still a work in progress. There was a significant amount of rust in the tank that kept clogging the float bowls in cylinders 1 and 4. Gas would leak out of the pod filters for cylinders 1 and 4 and I would have to clean rust out of the float bowl valve even when I took the bike for a ride down the street (I was doing a bunch of work to the bike at the time).

Anyways, I got to work with not too many issues - it died on the highway because those damn float bowls were clogged, but I made it there safe. On the way back, I was about 2 miles from home when the bike started bucking like crazy and I noticed the exhaust was glowing red.

Turns out, cylinders 2 and 3 were not getting any gas and overheated significantly and ruined the engine (and the exhaust). I didn't inspect the carbs until recently - remember this happened in October - and all of them look to be in good order. No tears in the diaphragms, all the jets are clear, nothing looked wrong with them except the finish on the upper chamber covers for carbs 2 and 3 show evidence of extreme temperature.

Is it possible that something else caused the cylinders 2 and 3 to overheat? If rust was clogging those carbs, I wouldn't expect carbs 1 and 4 to not have overheated the way the inside two cylinders did. It appears gas is fed to carbs 2 and 3 (inside two) before 1 and 4 (outside two) because the fuel line is in the middle. I don't see any rust in any of the carbs so if there was rust blocking the fuel line (post fuel filter) then it would have affected all 4 cylinders the same way.

Too Long/Didn't Read (TLDR); Is there any other cause for overheating in cylinders 2 and 3 other than clogged carburetors?

I replaced the engine and I am going to use the same carbs, so I am nervous that I will have the same problem and ruin this new engine. But don't worry... I've completely cleaned the gas tank of all rust.

air leaks at intake manifolds ?

You realize of course that pod filters cause the engine to run extremely lean (which leads to hot). Did you install a Dynojet kit and quality pods like K&N's? And if not it's highly recommended.

The intake boots were new and they did not have any leaks at them.

As for the pods, I have K&Ns and a stage 3 Dynojet kit installed. I was running a Vance & Hines exhaust with the pods. The V&H alone requires a stage 3 jet kit, so maybe I should have gotten even larger jets because of the pods?

Currently I have a Delkevic exhaust, which states that it does not need a jet kit, so I was hoping that I'd be alright as is.

It's probably lean. I have the Delkevic also, and no matter what they say, if does breathe better with all of the baffles intact, while A/F mix leaned out. My pipes turned blue immediately. I rejetted last week from stock 122.5 jets to the "racing" 125 jets, and it still seems to run lean. It does run like a bat outa hell and pulls like a freight train, but I am concerned that sustained higher speeds might start to burn up internal parts. I also noticed in my Kawasaki service manual that the J1 model used the #127 jets, so I may have not gone high enough. Just a tidbit of my re jetting / Delkevic blues.

If it was lean, then does it make any sense to decrease the air main jet? To restrict air flow? Just wondering if it works the other way around.

Also, I'm working on a KZ750, so the jets are probably different sizes. According to my manual, these are the jet sizes.

According to the DynaJet manual, the stage 3 jet sizes are #122 and #136.

Keep in mind aside from vacuum leaks and lean A/F mix, remember that #2 and #3 are in the center of the engine, therefore run hotter than #1 & #4.

Also make triple sure your fuel tank is absolutely clean. No matter how many times you clean your carbs, they will continue to plug, if your tank is contaminated.

Some bikes use a different finish on the #2 and #3 carb tops. That may be normal. If it got hot enough to alter the finish on the carbs, I would expect a lot more melted rubber/plastic.

I went ahead and got the bike going first try without altering the carbs even a bit. And lemme tell ya...

It's all around better than before. It's quicker, it responds better, and there's no popping/backfiring (so far).

I forgot that when I was taking the old engine out that some of the wires connected to the ignitor had disconnected due to rot. I did a maintainence on the wiring so it was easy to forget. I think that there were many different issues going on that caused it to overheat, so I think this thread can be deleted. .