using ford gears and a ford limited slip will make the install easier for who ever does it. The gears and limited slip will be machined to the specific dimensions and tolerances to fit Ford housings. I have no facts to back this up, but it seems that you see less people posting complaints about noises and such when they use the Ford parts. When you start using the non-Ford parts with the aluminum IRS housings it seems that it requires greater skill and knowledge to get the set-up right.
As JP said, I do not think it matters from a reliability perspective until you have high HP engines and drag race allot. Think about it, all those high HP stangs have Ford Racing gears from the factory.