Ford cruise control reacts strangely to some engine mods. You sometimes get a pulsing effect when a Cobra or GT-40 intake is added, which is the reason that the '93 Cobras didn't come with cruise. When you add a cam, all bets are off - a pulse is an almost sure thing depending on how radical the cam is. The fact that your cruise acted normal with these mods for three weeks is what surprises me. The mods affect engine vacuum, which the cruise servo is sensitive to. You might try plumbing a vacuum reservior inline with the cruise vacuum supply to soften the signal, but I don't know for sure if this would work. If it does not, and you really need cruise, there is an aftermarket unit made by Dana that is all electric, no vacuum, is adaptable to all cars, and can work with your factory steering wheel controls and VSS input.
P51C