After my runaway I have installed a 2nd lift pump (first was leaking around bowl seam) and tractor (L3940) is running fine. My problem now is fuel appears to still be getting into the crankcase, even when sitting the level appears to rise. What could be the culprit allowing fuel to get to the crankcase while sitting?
Did you install the stock (Kubota) lift pump? Or, an aftermarket lift pump?
I had an issue with catastrophic leaks of fuel into the crankcase on my Cummins. "Catastrophic", because I could monitor the incident by watching the stripe of fuel being deposited on the roadway in the rear view mirror (escaping from the crankcase vent)!
The issue was that we had installed an aftermarket fuel pump which was pumping WAY more pressure on the outlet side than the injector pump wanted. That pressure pushed the seal out of the driven end of the injector pump, and caused it to pump fuel into the crankcase. Actually happened twice, about a year apart. The last time, it happened when I was in the Harbor Tunnel in Baltimore, and I was forced to drive ~5 miles before I could pull over and stop. Didn't seem to hurt the crankshaft...
Even if you used the stock Kubota lift pump, the improved performance of the new pump over the one you replaced may have overwhelmed tired seals in the injector pump.
My last question is: when was your injector pump rebuilt? WSMs recommend a service interval (including seal replacement, of course) on the injector pump of around 1200 hours, I think.
Before anyone points out that a Cummins motor is not a Kubota motor, they both use Bosch injector pumps, and on both motors, the driven end of the injector pump communicates with the crankcase.
[Maybe a better design would be to have a vent to the outside between two seals on the pump shaft.]
-Paul