In my experience, the little bugs show up early in ownership and once corrected hopefully do not return. My new
B3000 showed up with a loader valve that was puking hydraulic fluid. Dealer came back and fixed it (then failed to check hydro fluid level - really?). Then I had a leaking fitting on the backhoe, tightened that one up. Then found a bolt had come out of the backhoe frame. In all of these instances, the dealer was to blame, not Kubota. I wish they had taken the time to set the tractor up right but they didn't, now they won't get another sale from me.
Since then the tractor has run nearly flawlessly, other than an AC switch that went bad. Replaced under warranty.
I hope your problems are behind you and your machine is near perfect for the future.