Clears fine, Ive got about 1 3/8" of space. Im going to swap to taller TCP motor mounts becuse my headers are real tight and ratlle on the shock tower. For the intake Im using a c&l intake tube and air meter, if you use the Ford plastic tube there is a little more room. You CANNOT run the factory EGR spacer, just not enough room and you'll need a eliminator kit to prevent you from getting a code. For the explorer engine, I hope youre not trying to run the Explorer EEC system. The 87-93 EEC IV with an A9 processor is by far the best route to take in a conversion into a vintage mustang.\ the Exporer OBDII and variable flow fuel pump would be a nightmare.