Welcome to the forum.
You've asked a question and the last thing that I want is for you to feel that I'm arguing with you or trying to tell you what to do. It's your tractor, not mine.
The word "restore" is highly subjective. To me, it means that you take the tractor apart, do whatever it takes to remove grease, oil, dirt, rust and paint prior to performing repairs to each item so that it is just like it was when Case put it together at the plant. When you deviate from that, then it is not a true restoration.
The engines that I've encountered are painted either Flambeau Red or Kohler Black and that includes all the bolts that hold it together. Therefore, the finish on the bolts isn't all that germane to a restoration. In my opinion, Grade 5 bolts do not make good head bolts. Grade 8 bolts would be more desirable. The difference is the tensile strength between the two grades. IMO, you run the risk of those Grade 5 bolts stretching and therefore, loosening. If this happens, then you will suffer blown head gaskets because the head won't be squeezed down tight enough to keep hot gasses from leaking past the gasket.
I'll be interested to read what KenC will have to say, as he has done quite a few Kohler rebuilds.