we went through the same problem with our 351w in the mach 1. there is only one set of heads that will fit the gt40p heads and still have clearence for the spart plugs. They are a set of shorty headers made by ford racing. Last time i checked, maybe 4 months ago, they were the only ones that wound fit without any issues. We actually took the gt40p's off and went with roush racing heads so we could get a set of long tubes to work. Hope this helps.
~ Performance Red, New Mach 1 (Mag 500) rims, Dual Flowmaster Exhaust, Black Letters & Rocker stripes, Sony - Rockford Fosgate system