I'm sorry to say, but you will definitley have to start over. The problem with using any type of filler to smooth the edge of the scoop into the hood is that body filler (fiberglass or otherwise)and metal have different heat dissipating properties. This isn't a problem on a fender or a 1/4 panel...but remember that the engine is right under there and the hood temp is constantly fluctuating. Over time, as the filler shrinks and expands it becomes extremely brittle and will eventually crack. Then, water will drip down into the crack...and oxidation will occur. Rust (even only a tiny bit) will take hold on the metal underneath and will continue to oxidize the metal under the body filler that hasn't cracked yet (remeber that filler and primer are not waterproof). It wont be long before more cracks appear, and the body filler begins to break off in chunks do to lack of adhesion to the rusty metal underneath.
When I bought my car it had a riveted shelby scoop to the steel hood (and it had the exact problem you described). By that point the hood was no longer salvageable (the riviting job and bondo work was horrible), so I just replaced the hood.
IMO, the only acceptable way to add a hood scoop to the car is to just buck up and buy an entire fiberglass unit with scoop molded in. That way you get something functional and long-lasting. I wasn't prepared to spend the money at the time...but I love the look and will eventually get a shelby hood or cowl induction unit.
Hope that helps, good luck 
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1965 Coupe: 351W, comp cam, Aluminum Systemax II heads (2.02/1.60), 1.7 Cobra full roller rockers, Edelbrock intake, Holley 650 double pumper, Mallory Unilite, MSD-6AL, MSD Blaster 2 coil, MSD heli-core plug wires, Hedman headers, 2 1/2" exhaust (GT style) w/ 40 series delta flows, 69 C4 w/ shift kit, shelby traction bars, 3.55:1 rear
Daily Driver:
1989 GT- 5spd, K&N (no silencer), Shorty Headers, King Cobra Clutch, Flowmaster Force II Cat-back
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