I thought about going oversize and a lower grade bolt, but with welding it up (if it works long term) then there is nothing special to remember, and the right bolt is the one spec'ed by Kubota. Do you think that the welded up and redrilled hole will not hold up as well as the original hole in the bushing?
I wondered if the fan flange with what looks like a bushing was a rubber mounted bushing within the flange to absorb some shock loads and possibly not shear the bolt on that occasion.
I don't think what you have done is wrong, rather your work is a first positive finding and you are to be commended for sticking to it.
RE your thoughts of going back to the bolts with more thread and thread in the shear area.
In my first 8 years as an engineer, I worked for the Canadian equivalent of the National Transportation Safety Board and my job was to find the cause of the worst motor vehicle accidents.
What I took from that job was this: just because you got the same part from two different sources, did not make it the RIGHT part as determined by the engineer who designed the shear flanges or equivalent assembly.
Parts supply chains all over the world are corrupted. Non legit parts were even found on Obama's Air Force One plane.
Right now you have a working unit. In the beginning your initial thoughts had to do with sand gravel and small stones. Others like me said you should be able to blow sod.
Leave it as it is for now. When you get past winter, then stand in front of your running blower and throw shovel fulls of sand and small rocks into the blower. I will be very surprised if the shear bolt broke.
As far as the bushing in the fan flange is concerned, ask your dealer's parts guy to go back up the chain and send him a photo of a new fan to give to you Then you will be certain what was there originally and can decide if your repair needs to incorporate the bushing feature.
Dave
M7040