This is difficult to discuss without seeing it, Elaine, but let me give you some background. Square cut nails are still available. They do tend to stick above the wood and can be difficult to sink below the surface of the wood. They will also tend to split the wood if they are sunk into it. Floor sanders use sandpaper that is coarse for the first operations and finer as you get the wood smoother. The sandpaper is expensive and will be torn or otherwise hurt but the nails if they stick above the surface. If the nails are really bad, they can hurt the sander.
Since your pine probably was not dried in a kiln, it may even still have a lot of resin in it. This will tend to make most finishes not adhere to the wood. Nothing to base the following on, but I would make a small wager that one of the coats of paint on your floor now is milk paint. This is a predecessor to our modern paint and it's use goes back to the time of early Egypt, or more than 2000 years ago. Most of todays paint strippers will not touch it. One that will is Peel Away 1. Check www.oldfashionedmilkpaint.com, I think it is, for more info on this. Milk paint is still made by a specialty manufacturer and their site has tons of good info.
Elaine, I really don't know what to tell you from here. Perhaps you might want to see if anything above sounds interesting.