Difference between stock heads and GT-40P's?

[Shotgun28]

I was trying to figure out in relation to size why my Flowtech headers will work on my stock heads, but won't (supposedly) work with the GT-40's? what exactly is the difference. If anyone uses Flowtech Headers, what Heads will work? Thanks everyone...

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91 LX Convertible Gray on Red B&M Shift improver kit, March underdrive pulley's Richmond 3.73 gears, 1 5/8 Flowtech long tube Headers and off road h-pipe, Flowmaster 2-chamber cat-back with S.S exhaust, MSD 6A Ignition with coil,Cap and rotor, Taylor Pro wires, K&N 12" conical filter system, Jet stage 2 performance chip and Lentech Street Terminator plus on it's way...just ordered some new Red alum pulley's. Doing some big shopping of late, I will keep you posted.