I'm coming in late to this thread, but can empathize with your frustration - with the attachments you have listed, shop time is a poor substitute for quality bota time and knocking things off your project list.
I've got a B3350 - the precursor to your model. The B3350 is notorious for DPF problems and at just under 1,500 hours, mine has been replaced twice. After the 2nd replacement, I was instructed by my dealer and the regional service rep to run the machine at full RPM's at all times. I'll let it run at ~1,700 RPM when I start it for a minute until the first engine temperature bar appears - then it's wide open for the rest of the day. Have not had to replace the DPF since adopting the new operating procedure.
At some point, I also had a problem with loss of power like you described and was also blowing the 5 amp panel fuse. The fix on that was to replace the PTO and hydrostatic safety sensor/switches. With this problem the machine made 2 round trips to the dealer, but they did get it.
Maybe you could escalate it to the Kubota regional service rep?