Sorry I had to cut this post up, it wouldn't fit on one posting.
I'd say you could pay anywhere from $300-$450 to have the hood painted. Maybe less if it's already primed. You could easily spend close to $700 for a new hood.
The cost of paint all depends on who does it. For a used hood, the shop is going to have to wet sand the hood, prime it, then add the clearcoat. A new hood usually comes primed, and just needs the paint. A place like MACCO probably isn't going to do the best job. If you know of a reputable shop near you that has a paint/bake booth, I'd have them do it. It may cost more, but you get what you pay for.
My local body shop is really good. They can get a factory match on the paint, not 1 or 2shades off, and they have a full paint/bake booth. They also were honest with me and said that if I painted just the hood, it wouldn't match the fenders or bumper, and be noticeable where the ends meet. The best way is to have the whole front clip painted, so everything blends together, but that is expensive to do...and if it's not that important to you at the time, just paint the hood.
I got the hood from another forum member - Jimmy_Beaner. He was selling his old GT hood for a Cobra R hood...so I got if for a decent price, plus I didn't have to paint it.
Usually you can find used hoods anywhere from $100 to $300. Check around forums, ebay, some takeoff sites. To be honest, finding a sonic blue hood is pretty hard, I got extremely lucky. If anything, you could pick up a new hood from Ford. I think they run around $350, maybe a little more. I'd check Tousley Ford parts, Spector V always mentions them...you can get OEM parts for cheap.
There are two different hood scoops. The 99-00 version, which is smaller, and shorter, was offered on the 35th anniversary models, and the spring edition models in 00.
The 01-04 scoop was the taller, bigger one (the one I have). These came standard on 01-04 GT's and other models. You can put this one on a standard 99-02 v6 hood. It will fit just fine. The only issue is that the 7 or 8 studs that attach the scoop to the hood aren't marked on the v6 hoods. On a GT hood, the stud placement is marked, making the hood scoop easier to attach. I believe there is a writeup for attaching the hood scoop on the site, it isn't too difficult.
The 03-04 v6 hoods will not work with the hood scoop. That's what I originally had on my car. I replaced it with a GT hood (that came with the scoop).