Because you have included this line: TC_Configure(t.tc, t.channel, TC_CMR_WAVE | TC_CMR_WAVSEL_UP_RC | TC_CMR_TCCLKS_TIMER_CLOCK4); in your object constructor instead of your "setFrequency" function, there is no way to modify which clock is used for a given timer after the user has declared it. Here, you are using TC_CMR_TCCLKS_TIMER_CLOCK4 for every timer, which is the way cmaglie originally posted his example.
I am trying to figure out if this line can be moved down to your "setFrequency" function. If so, then adding in support for the dynamic clock selection will be really easy. :]
Cheers!
SRG