I run the ford motorsport 1.72's and I just had to pull the baffle off of the passenger side valve cover. Be sure to run the stock valve cover gaskets or ones that are steel embossed. I didnt do that and it walked out and made a mess at the track.
Or run the FRPP 6582-E302P cast aluminum valve covers and a 1/2" plenum spacer (between the upper and lower manifold). Moroso and Slummit off the same valve cover for a little less w/o the Ford Racing logo. Pretty much any rocker will fit under those. http://www.fordracingparts.com/parts/part_details.asp?PartKeyField=5688