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Did the problem start when you did the tranny swap? If so, it must be related...

It may be as simple as needing to short the two wires in the neutral start safety switch which you may have left hanging down, disconnected, near the tranny.
As Dave mentioned, the ECT computer (tranny computer, located behind the rear seat right side panel, above the rear armrest) interfaces with the cruise control computer. Maybe you need to change engine ECU's to a manual one and disconnect the ECT computer. Or just disconnec the ECT computer.... Not sure on that one.
I've also seen cruise control actuators (under the hood) develop vacuum leaks and stop working.
Long shots.... It could be a faulty cruise control computer in the right side kickpanel or a faulty speed sensor if you have a digi dash.
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