I would use Ford parts whenever possible. I've proven time and time again that local parts store parts have a lifespan of about 5 years max.
So if you plan to sell the car in a year, put the crappy parts on it and keep the receipt for the warrantee. If you plan to keep it forever, put Ford parts on it. But beware of counterfeit Ford parts - stick with a Ford dealer.
2004 CVPI - 85k miles
1997 T-Bird LX - 85k miles
1994 Supra Turbo - 107k miles
1988 T-Bird, 1995 T-Bird, 1996 Cougar