The factory Dual Media radio has an integral amplifier - it does not need an external amp. What was the part number of the radio you took out of your F-Series? Some of the radio models used in F-Series trucks have external amps, so you may have a compatibility issue. Other than that, I would recheck again all of the wire splices you had to make to put the '99 model electrical connections into your '97 model vehicle.
BTW, in order to seat that Dual Media radio into the dash of an F-Series, a little "massaging" needs to be done in the opening to remove a couple ribs above the radio in the substrate of the I/P. A "hot knife" works well, or you could probably do it with a small razor saw.
Regards,
cobrajeff