I Guess you are using pedel covers. I installed bullet pedals in my 97 GT. Very hard to do the brake and clutch but the other two just pop in. I kept the brake and clutch pedals in the sun let in soften the rubber and sprayed down the back with silacon spray and twisted them on with the help of a flat tip screwdriver.
__________________ 97 Mustang GTS Laser Red 5spd, MSD coil packs, Cross Drilled and Slotted Rotors,Ford Racing 9 mm wires, Ported and polished upper intake Plentium, 70 mm Accufab TB, Steeda intake spacer,
March underdrive pulleys,3.55 FMS Gears,C&L 80mm MAF,C&L Power pipe, Sub-frame connectors, Mach 1 tokcio shocks and struts, Mach 1 chrome rims with 255/45 17 tires, 125 HP NOS dry nitrous kit,B&M Ripper shifter,Maximum Motorsports lower control arms, 2 chamber flowmaster 2.5 in,BBK offroad X-pipe, 218.3 RWHP 49 | 
Pedal Covers 
I would say leave them in to install the covers.
