So, I finally bit the bullet and took the thing down to my local AgPower dealer to have it looked at. I initially went to the Kubota dealer a couple of doors down, but they wouldn't even give me the time of day. Nope, grey market import, go somewhere else.
IF Kubota think that I will EVER buy a new (or even used) machine from them in the future, they are VERY much mistaken. In my view it is unconscionable to turn your back on customers and refuse to help them AT ALL just because you had a tiff with some ex-partner 30 years ago. SHAME, KUBOTA, SHAME!
Anyway, it turns out that the pump I put in was stuffed. Apparently, the hydraulics on the L1802 (and probably the rest of the L series as well) are a beast to get primed and bled properly. The pump had run dry and chopped out. AgPower were't able to get a replacement (Kubota were no help at all as usual, AgPower asked me if I had a part number that I could give them), it appears that there are none of this $1400 item in country (seriously, $1400?). I took the old pump down to them, and upon inspection it was found to be in much better shape than the new one so they installed it.
After draining and flushing the transmission case, bleeding the hydraulics and adjusting limit stops and pressures, it's better than it was when I got it. Turns out that, apart from a knackered pump, the oil had water in it. The main culprit was the vented filler cap in the top of the transmission housing (The big one between the drivers feet).
The cap is supposed to have a rib along the centre to unscrew it with, but it's broken off on the one I have. What remained was a rectangular trough that turned out to be very efficient at catching rainwater and dumping it into the transmission case. I filed the ends of the trough flat, glued some paper over the base of the trough to seal it (leaving the air channel clear) and filled the trough with epoxy.