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i have a ferris mower with a kohler command 27 engine that loses power and eventually dies unless i pull the choke and it runs on for a bit then dies completely. i have changed out the fuel filter and installed a see thru one. when the motor starts to act up[usually when i make a zero turn] the fuel filter is not always full and usually it is only half to a quarter full. also when operating or trying to start it there is bubbles coming in, even when it is running.the solenoid is fine and i have cleaned the carb as good as possible without having to remove it. i dropped the fuel bowl and cleaned it thouroughly.i also blew out the tiny pinholes in the bowl body itself. when i pulled the outgoing hose that leads to the carb from the fuel pump when it is running there is times when the fuel flow is weak or sputtery.i havent cleaned the fuel tanks yet as i didnt believe they were much of the problem. the only thing that has happened is that we needed to syphon gas out of the fuel tanks for other machinery. would this cause a problem?we used a piece of garden hose to accomplish this. also the mower has been run completly out of gas several times. thebiggest stump of all is when i first start the engine for the day it runs great and has never run better since i did those cleaning things. it startes to do it after about 30 or so minutes and usually starts after i make a violent[fast] zero turn.also when it does start to act up if i pull the choke all the way on the mower will run quite normally for awhile longer.

Sounds like you have a bit of water in your fuel system.

Clear filters should be outlawed, it gets folks focused on things that are not a problem.

This may sound redundant but I would replace every fuel line that I could. It's inexpensive and would eliminate the possibility of fuel line cavitation. Cavitation is the formation of vapor cavities in a liquid i.e. small liquid-free zones ("bubbles" or "voids") that are the consequence of forces acting upon the liquid. I'm no expert by any means also. I did have one other thought that it could be the fuel pump is weak(ening) with heat or it may have some debris in it.