Dusty,
Good luck. Sounds like everything is going well. I was told one time that these guns were designed to hit a little low so they could be brought in by the shooter/ammo combo with the file as altitude is influenced by bullet weight, powder load, and shooter sight window preferrence. So far, I haven't shot my Freedom Arms enough to cause me to file the sight as it is a "permenant" alteration and I haven't yet decided on a final load. I was also instructed not to alter anything until I have shot my desired load about 500 times and am certain of its point of impact and my desire to stick with it for this very reason. However, my gun from the factory came with a front sight with sharp edges that would catch and clothing as the edges on it were very clean and sharp and serrated. I took some 220 sandpaper (fine grit) and BARELY "deburred" or "desharpened" just the slightest portions of the edges of my sight and like it much better this way...my sanding was so minimal that no one would notice it.
Chipster, A scope sits much higher on the gun (above the barrel) than does iron sights. Sights are above the barrel, but just barely. What I have found with sighted riffles is I like to be about an inch low at 25-30 yards in order to be on at 100 yards. I have no experience with scopes on a handgun.