I have a 61 c20 and had most of the same concerns that you have. But, I hunted for this particular truck and overpaid for it because its what I wanted. Now, I am $7000 - $8000 in and There is no turning back but I learned a few things along the way. The parts are harder to find for a 60-62 because some of them are not reproduced. I swapped to a 700r4 which is a nice auto but I had to pull my engine make all new mounts remove a crossmember and make a new one. As far as body work. I would recomend doing all the bolt on work you can and some of the hard labor prep and leave the body filling and paint to a professional. The money that I spent on tools and supplies to do my own work I could have paid someone to do it for me and recieved a better job. If you like the truck then you should keep it. If your not sure then go check out the 66. You never know, You could end up with two projects. If I had it to do over again, I would get a 64+ because of the thngs I wanted to do to the truck.
