If you don't plan on using the PTO, leave it off.
As to the bolt, the only consideration is that the threads inside the crankshaft end will rust if the hole is not filled/sealed.
Why dont you just go to a hardware or auto parts store and buy a bolt about 3/4" to 1" long and coat it with grease or anti-sieze compound and run this bolt in tight?

This way, if you ever need to put the PTO back into service, at least you will still have a good hole to work with.
Take the OEM bolt with you so you can get a bolt thread that matches the hole in the crank.

Thank you mownie. That is what I will do. I thought the bolt was to hold the entire shaft on. But now I see that it was just to hold the PTO in place. I am learning a lot from this little project. Thank you again.
Dayton