Injection pumps are not something you want to shade-tree.
If you think the pump is bad, take it to an injection pump shop and have it checked out. Odds are they will tell you it's OK because they rarely go bad.
Next you have to find out how to put it back on and time it. You'll need the Kubota service manual for that or someone on here who can step you through it.
My guess is probably what happened was someone ran it out of fuel and all it needed was to be bled.
Don't take this personally because I didn't. I know you didn't say I shade tree. You were just making a statement but I don't shade tree. I do it once, do it right, because I don't like covering the same ground twice.
As for suspecting the injector pump, at this point I don't suspect any one thing which is why I'm here asking you experts for some pointers. I'm not a lost goose mechanically and pulled wrenches for many years but am somewhat lost when it comes to diesels, especially troubleshooting. I understand the principal, have changed injectors, glo plugs and bled systems of air, just general things but never have gotten into troubleshooting so here I am. For starters the bowl/filter/attaching nut on the fuel/water separator are missing so someone bypassed it putting the fuel line straight to the lift pump. Not causing my fuel problem I know but that IS "shade tree." I thought of it having been run dry of fuel but having a lift pump wouldn't cause no fuel at the inj pump, lift pump side, unless that pump is bad. Tomorrow I'll pull the injectors so it'll free spin and start with the lift pump and see if it's putting out. I absolutely need what you said, a shop manual to time the pump but haven't found one online. This mower, besides being pretty nice with only 527 hrs, assuming the meter works, has a 73" cut so it's a hoss and I want to put it to use!