I have had my BX2750 for many years now, and the pto shaft has never hit anything be it up or down. I don't know what tractor you have the blower on, but on by
BX22 and
BX23 it is engineered perfectly like I would expect from Kubota. I have to agree with some others here, something is not assembled correctly. I just refuse to believe that Kubota would send something like that to market. There would be just too many issues down the road with a error like that.
One other thing, you state that is says in the manual not to raise the blower with the pto running. Or does it say not to raise the blower while blowing snow? You have to be able to raise the blower while the pto is running so you can turn sharp corners without plowing up a bunch of gravel and also while backing up you would not want to drag the blower backwards. I questioned my dealer on this very thing when I bought my big blower, and he explained it to me that they don't want you raising the blower while in the act of blowing snow. In other words, while the blower is full of snow. When you have to raise the blower, before doing so, stop forward momentum, let the blower clear itself,then raise the blower. This has always worked for me on both my front mounts without any problems for many years now. He made is sound as if Kubota's concern was not to raise the blower while full of snow. Not sure if they are concerned about the additional weight of the snow, or possible extra stress on the auger. But I assure you, to get through drifts up here (MN), it is quite often necessary to raise the blower as high as I can and cut the top of the drift off, then back up, lower the blower and get rid of the lower half. On page 21 of my owners manual under the heading, Snow Removal Methods, it even spells out this process
I'm guessing you will find some assembly issue with your blower. Good luck.