[Xeen]

Ya know you could just buy reproduction short bed sides and just shorten the steel floor and save yourself a nightmare trying to weld and bodywork the bed sides.
The short bed sides will cost $1100 shipped but it will save you a ton of time and headaches.
You said you got a great deal because of the blown motor when you bought it so spending a little money on reproduction bed sides won't hurt that badly.
I would be careful about which manufacture you buy the bed sides from though because a lot of them are out of china and don't use the OE gauge steel.