Welcome! Congrats on the new bird! When you get a chance, send Geoff (site admin) a picture to join the on line car show (you can update as the car changes)
What I usually tell people is do the major things you HAVE to do right now, (like the front fenders and figure out the tranny right now) and then research all the things you WANT to do and as you go, you may find that you might want to do things a bit differently that you originally thought?
Get the new fenders (NOS, good used or aftermarket) and get the car all cleaned up and looking and working ok. If you can figure out the tranny issues, then good, you are set until you can collect all the info and the parts needed to go manual. There are a few different 5/6 speeds out there many with true overdrive final drives, so do a little research on that end to find just the right combination for you. (Maybe figure out what rear gears you have first?)
The drive shaft will most likely have to be changed... so just expect that. And the cross member will more than likely need to be changed, and should mount with out actual modification in the end. (maybe double check to make sure you don't have an O/D auto in there right now?) They usually require a different cross member etc...
But, the good news in the fact that your car has been changed with each owner is, that you have complete and total freedom to change and or modify the car to suit your needs with out decreasing it's value say if it was an original survivor car etc...
So I say, do your home work, get all the info you can on what are the best mods for the money, what others are doing successfully, and then make your plans, and just go for it! Build the car of your dreams!