Ford and some other after-market companies have been teasing us with proto-type heads and intakes, but so far, its all show and no go. The SVO intake/heads are the only ones currently available for the SOHC. There aren't any for the DOHC.
The SVO parts do work well, but are pretty expensive. Most people just go with the 99 GT parts, which work almost as well and are a lot cheaper.
Most hard-core DOHC people end up just modifying, porting, and regrinding the stock intake, heads, and cams. The Cobra block and crank really are that good. The rods and pistons need work. But there is a good after market supply of those.
Aftermarket heads, cams, and intakes would be nice, but really, if worked stock parts are hitting low 10s or even 9s NA... A Cobra R style air-trumpet intake manifold would be nice though.
Check out:
http://www.seanhylandmotorsport.com