Read the article
Adjusting Rotary Cutters for information on setting up the cutter.
You cannot cut it shorter than 3" with a rotary cutter. As tall as the grass is you may have to make 2 passes but I would try it for a few feet set as low as you want the final cut, you might make it in one pass depending on what type of grass it is. If it bogs down too badly then you will have to set the cutter up as high as it will go and make the first pass then lower it for the second pass.
The rear wheel rides on the ground.
PTO RPM should be 540. Do NOT under any circumstances try to use the 960 RPM PTO setting! In fact, the 960 setting should be blocked out and you would have to loosen a bolt and move a metal blocking piece to get it in 960 but since it is a rental unit it may be possible to put it in 960. Again, DO NOT do it.
Adjust your ground speed so that the RPM's stay up. If you hear the RPM's drop you are going too fast.
If you are not sure what is in the field you might want to be prepared to hit the clutch if you hit a big rock or other foreign object.
Watch the height of the 3 point hitch. Most Kubota 3 PH's will drift downward after a while and you may have to raise it periodically.
To engage the PTO drop the RPM down to 1,200-1,400, push the clutch in, engage the PTO, let the clutch out, then speed up to PTO speed. When you are ready to stop leave the PTO engaged and slow the engine to idle before disengaging the PTO, the engine will slow the PTO and cutter down.
Safety tip: Do not get off the tractor until the cutter has stopped spinning completely. A rotating PTO shaft is extremely dangerous if you get near it.
Do NOT let anyone get near you while operating the cutter. The tip speed on a 5' cutter is about 12,000 feet per minute.That is roughly 135 MPH and sticks, rocks, and everyting else can come out from under the cutter at over 100 MPH. Do not park your vehicle near where you are cutting. The only dent in my wife's 2004 Jeep Liberty was put there by a chunk of wood thrown out from under a rotary cutter we passed by on a highway in Mississippi.
Downed grass: Learn to love it while it lays there turning brown. This is a rough cutter, not a finish mower.
BTW, a rotary cutter blade is not sharp, it has an edge approximately 1/16th" wide. It is make to tear the grass, not shear it.
In case the cutter starts vibrating badly while operating disengae the PTO and let the cutter come to a complete stop and try again. Occasionally, and depending on the brand of cutter, grass will get wedged between the blade and the "stump junper" (big round plate blades are attached to). Once in a while it will clear it self by just stopping and starting over. If it does not clear you will need to stop it, raise the 3 PH to maximum height, SHUT THE ENGINE OFF AND PUT THE KEY IN YOUR POCKET, then put your gloves on and look up under the cutter and wiggle the blades around until you clear the grass out. My old cutter used to get hung up regularly and the easiest way to clear it was with a hose nozzle to blast the grass out from between the blade and the stump jumper.
Hope that answers some of your questions. And, I hope it was not too elementary but I was assuming you had never operated a cutter before so I tried to cover the basics.
Above all, please be safe. Tractors are wonderful and I love my rotary cutter but it can be a dangerous piece of equipment. If in doubt about anything the first rule is stop the PTO, stop the engine, and then think, think, think. Most so called accidents are not accidents at all, they are mistakes made by operators. Even the most experienced operator can suffer from a momentary lapse of memory and get in trouble.
If you feel yourself getting really tired get off the tractor and rest. The work will be there tomorrow. A tired operator is a dangerous operator. When I find myself doing something stupid, or find that I am "fighting" the tractor I know it is time to park it for that day. I have never regretted quitting but I have often regretted continuing when I know I am too tired.
Bill Tolle