All I had to do on mine was remove the baffle inside the passenger cover. No grinding or clearancing, just unbolt it. I'm still using the stock valve covers.
Like Eagle said, the real key is make SURE you have the EFI covers. Otherwise, sell them and buy the EFI version. My two cents.
1988 LX 5.0 5spd Moonroof
Tri-Ax shifter, CAI, 75mm Granatelli MAF, BBK 70mmTB, 24#, BBK fuel press regulator, RPM II, Cam Research custom, 170 TFS Twisted Wedge heads, 1.7 TFS rockers, Electric fan, A9L, Diablo Revolution chip, MSD 6AL, BBK long tubes, 2.5" X pipe Magnaflows no cats, Auburn 3:73 gears, lowering Ford C springs, bump steer kit, MM CC plates, MM braided hoses, BBK rear control arms, Eibach sway bars, sub frame. Cobra R hood. 10th anni wheels w/245s, 140mph Speedo.