My M9 is also a 2 speed PTO but the 1000 21 spline drive is a separate shaft that has to be inserted when the 540 6 spline shaft is removed. Yours possibly is the same way. Easy to tell by looking at the output end of the PTO.
If there is an external spring clip against the outer PTO shaft bearing, the shaft is removeable. If no spring clip it's not. If you bought the unit and it did not come with the 1000 rpm shaft, you'll have to purchase one from a dealer who can order it from Kubota. Be apprised that it won't be cheap.
If it is removable, you'll need to back the tractor up an incline so as to put the front end lower than the rear (I use a set of heavy duty truck ramps) and then remove the spring clip with a pair of needle nose pliers and pull the 540 shaft out.
You need to raise the back so your fluid don't run out. Insert the 1000 shaft, turn it until it seats fully and replace the clip and you will be in 1000 rpm mode.