My manual says to bleed lines by just pumping on the primer pump on top of the fuel filter. It doesn't say to open the injector nuts and allow air to escape. I am having air collect in the fuel/water separator bowl. Tractor will run for 30 minutes or so before it dies. I can bleed the air out by following the manual but it collects again. Am I just not bleeding it properly, or is it likely it is sucking air into the system somehow? All my connections seem to be tight.
It sounds like to me that you may be getting air form a bad connection. As you know the injectors are higher than everything else you mentioned and the air bubbles are not going to go back down, they always go up.
Kubota engines will consume quite a bit of air and keep on chugging till it bleeds out. Most people are able to drop the filter and install a new one with out ever having to bleed anything.
I think you are going to have to find the leak, may be lots of fun!
Check all hoses and connections. You might even have to use a vacuum pump and do leak down checks on lines and hoses.
I don't think it will be that hard to find.
Scott