Thanks everybody for the help and tips.
I found some pdf's and a good video (
remove the top cover video) on removing the top cover on these pumps to do a reseal if yours was leaking. Mine was not leaking but I had to take it apart to get the throttle shaft out. It maybe could have been cheaper at a different place but probably not by much. If you need some work done in or around Charlotte, NC, give the guys at Carolina Diesel Service Of Charlotte a try. They were very helpful and informative over the phone and in the store.
The hardest part was getting the return line off the top of the pump. The nut would not spin on the plastic line going into the top of the pump cover. I held it with pliers and tried turning but nothing would happen. I thought I had actually cracked the line holding it with the pliers. I ended up just pulling the top cover up and out from the tractor and twisting the cover off. It turns out that the little plastic sleeve that the nut tightens down on had gone up in the nut just enough to make it not want to turn on the line. Also there is a brass plug that is in the end of the line so with it and the plastic sleeve, it could have had the nut tight. I pulled the brass plug out and then the sleeve off the line and the nut started to turn freely. I was so upset with myself during the day because I just thought I had screwed something else up or broke another thing but it turned out everything was ok at the end of the day.
With all of gaskets and the throttle shaft, I think the total was right at $61. The old shaft had some bend in it but didn't seem enough to cause it not to run properly. I doubled and tripled check though that the springs were put back in the right holes in the governor and throttle shaft and we put it back together. I could tell though after getting the cover back on, that it seemed to be fixed before even cranking it because the throttle shaft was trying to turn in way more than before to go down to where it was supposed to idle at.
Anyways, it cranked up and ran great since it was throttle where it needed to be and was really screaming at first since the high throttle idle screw was way out so I proceeded to adjust both of the screws to fine tune them in to where they should be set. I've got it idling around 800-850 and at full throttle, it's staying right near 2300 with the needle maybe bumping up to 2350 but staying closer to 2300. We can always adjust them again if something changes but I think it's probably good to go.
The knock the tractor had when I first posted my initial message has seemed to go away? I guess since it was running at a very low idle the other day, it maybe just wasn't turning fast enough or something was causing it have a noise, I really don't know what it is or maybe it just quit but the knocking noise was gone. We couldn't hear from standing around or putting a broom handle(wood stick) up against where you could hear the noise before.
Hopefully everything is good now and the tractor will lasts us for years to come. Not really sure it needed a clutch, it had some wear but it wasn't gone, but it maybe had been slipping. Either way, it's fixed and I don't have to worry about it coming out in the near future.
Once again, I appreciate the help and insight!!!
Charlie