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is the msd box the same type that was used on the dyno?
if they are different likely one is retard and the other advanced.
analog amplifiers are ran with ign retarded, digital are advanced.
put a timing light on the balancer and check timing and then switch the wires and see wether the spark advanced or retards, this will tell you where your wires should be corresponding to the type msd unit you have.
check your timing none the less and see wether it has changed.
hth
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