Hi there
Without knowing exactly what PTO shaft you have, I can only talk generally.
There is no real rule of thumb for the length of a pto shaft and it does depend what implement you are connecting, is it mounted on the three point linkage or trailed on a hitch.
Ran my conventional JD459 baler behind a new tractor and the pto shaft was too long so we simply shortened it a bit so that it would not "bottom".
You just pull the shaft apart and also remove the safety sleeves to reveal the inner drive shaft tubes that fit inside one another. The cross section of the shaft tubes will probably be like a "lemon" ie circle with two lobes diametrically opposed. You will see what I mean when you actually see it.
Offer up the inner and outer metal pto shaft tubes, that is both ends, now that you can actually see the inner metal shaft tubes, and decide how much you want it shortened by. Just cut the same amount off the outer and inner shaft tubes and also you may also have to trim the outer plastic safety tubes by the same amount too. It could be that you may only have to trim the outer plastic safety sleeves as that may be why you think the shaft is too long.
Be sure to remove the burr on the tubes and put a bit of grease on the shaft tubes as they fit together when you re-assemble them.
It is preferable to make the PTO shaft as long as possible for strength ( max amount of "lemon section" metal inner shaft tube inside outer shaft tube) but be careful that it does not bottom if you raise the lift arms or in the case of a trailed implement, operate over undulating ground. This will bend the shaft if it is rotating.
Pretty sure that will fix things.
If you ever need to replace the "lemon section" tubes because they are bent or too short, the inner and outer tubes can be brought from any decent agricultural machinery dealer by the metre and the two uj joints fitted to the ends usually with roll pins.
Stew Edwards, May 2010