Your unit should pull like a Willys in 4WD regardless of the hours.
There are several posts regarding the cable arrangements for the engine throttle and the transmission selector on the trans case. If they are not synchronized correctly or have too much slack in the cables then you'll have problems. I think there are some posts regarding oil temperatures, too, for the trans. Use the search function and type in "no power", "low power", etc.
I take it that your ball picker runs off the hydraulic circuit for accessories. Since the trans and the accessory circuits are separate they should not be affecting each other. IS the engine running hot or is the floor of the bed really hot?
Two Guns has good point that you might have something caught up in the Trans filters.
I can't think of an easier chore for a 900 than running slow in low on a flat driving range...
If worse comes to worse call Kubota directly.
Once you get it straightened out you'll really appreciate the fuel savings and ease of handling.