This is kinda long ...
I am in the market for a compact. Since the market is as it is, I have not bought yet. Not only is the pickins' slim, the price asking is not practical, and it is non-negotiable too.
I will try to help, but I am sure others have already said this. First, the lower arms on the three point hitch. If they rub the tires, either one, THEY ARE NOT adjusted. The sole purpose of the pin and chain adjustment is to prevent rubbing the tires. If you look at the pin adjustment, you should see adj holes and a slider slot (use only one slider or you will have slop) - This slider allows you a little lee way in hook up. Pin pin on one side and some movement to match other. My tractor is an L4701 - one step bigger in hp and frame that the 3901. But I think the 3 point is probably the same. In the pictures below, T1 is a picture of my 3 pt. The top link is upper middle (silver color) and the lower arms are the two that are the lowes in the picture. T2 is the Left arm and stabilizer. Note that only one is in th slot adj. T3 is the right arm. T4 is a Pat's quick hitch. Lets me hookup without matching hitch pin and arm holes.
Next, the whine you mention is normal. But since these machine are best run at full rpm, I don't notice it.
Next the emission thing you mentioned. It is the tier 4 epa method of filtering out diesel particles before they enter the open air. The particles collect in a filter mounted under the hood -Diesel Particulate Filter, thereby called DPF filter. The filter needs HEAT to burn off the particulates. If you run the tractor at full rpm, it will rarely need to regenerate. If you run it a cool - low rpm - it will not burn off particulate and need to eventually do it for you.
Insurance - If you purchase new from a dealer, Kubota will offer you what is probably the best insurance in the business. It covers a lot, including theft and roll over. But you can do that ONLY as long as you carry the note with Kubota - 60 months interest free.
While you are looking, you should look at the 2501, as well as the 4701. The 2501 and 3901 only differ in the hp rating. The 4701 is a larger frame, different hydraulics and capacities. If you plan on working a lot on a gravel or dirt road, moving gravel and dirt, the 4701 may suit you better because of the difference in hydraulic capacity.
Tires. In the picture, you can see my tires. They are R4 industrial. Tires are a option when you buy a new tractor. Ag tires are the farm tires we usually see for plowing and traction. R4 industrial tires are smoother, but also have traction - probably the most popular non- farm tire. Then there are very smooth riding turf tires for landscape work. Will not tear up the yard.
Last, I would be remiss if I did not mention that there other fine tractors other than Kubota.
Long, but I hope that helped somewhat.
Best wishes, Larry