I had this exact problem with my F2260. You said you replaced all the fuel lines, I just want to inquire if you truly replaced "all" the lines. In my case I did nearly everything you did before replacing every fuel line. It turns out that the rubber line that crosses over the top of the transmission was collapsing due to heat, heat that is only experienced when you engage the PTO and operate the unit for some time as you described. The combined heat of the HST and PTO operation was the only thing that would cause the issue.
I had the rusted metal pickup line inside the tank as well. Cleaned all, replaced filters, replaced cap.
Once I had replaced all the fuel lines - some were a bugger to get to - the problem was solved. It sounds like you almost experienced the cure after replacing the fuel lines. Are you sure you got all of them? And did you use a high quality hose?
Your machine is likely about the same vintage as mine. I had the problem two years ago with around 500 hours on it. I think it's a matter of the age of the rubber hoses more than anything.
FINALLY SOLVED (Please see my earlier post)
Before I go into details on what the problem was, I would like to thank all those folks that tried to help me out. Two of the suggestions were actually what solved the problem.
The problem was debris in the fuel tank that was not removed when I vacuumed out the tank. I had sent to Kubota all the details as they appeared in my posting and they connected me with Dennis Hood in Georgia who is the Kubota customer service rep. Dennis has been in the business for almost 30 years and took the time to discuss all the issues. He suggested using a 渡ursing tank to try and see if it was an engine problem. This had also been suggested by a contributor to my post so I got an empty gallon water bottle, made the connections to the mower and gave it a go. The mower ran without a problem for over 3 hours and several gallons of fuel. Dennis thought the tank may have had contaminates in the fuel that would have left a deposit on the tank that would subsequently clog the fuel line. I removed the tank and dumped the contents in a bucket. What also came out was an accumulation of dirt, rust, and pine needles. I have no idea how the pine needles got in the tank but I got the same thing when I vacuumed the tank in the summer. I took the tank to a local car wash with a pressure wand and cleaned the tank for 15 minutes under high pressure. I let the tank dry completely, replaced the fuel rod with a single piece of stainless steel tubing and put everything back together. Bled the lines and the mower started right up. I mowed the entire 3+ acres in 90 minutes.
Hats off to all the helpful suggestions. The removal of the tank was actually just two nuts that held a strap around the tank, so it was much easier than I thought. As Dennis and other have said, 添ou need 3 three thing to get a diesel engine running, air, fuel and compression. I hope that I can keep this mower going as long as I have had my B5200 going which will be 28 years next mowing season. Thanks to all for their help.