Hey Dano,
This truck is definitely a 66 styleside. The hole in the side of the bed is for an optional step which I don't think is all that rare or attractive. I would weld it shut and smooth it out.
I also have a 66 F100 shortbed styleside. It's a great little truck.
You can also find out tons of info about the trucks at a couple of Ford truck forums. Here's the links if you wanna check them out:
www.fordtruk.com
www.ford-trucks.com

All the best.