Hi, I am also trying to make a frequency counter using msp430F513X. I am curious about that why your program is based on two timers but not using a capture mode? I see MSP430F550x timerB does have a capture mode and I think it could be simpler when you use only one timer.
For now I am using capture mode to make SMCLK measuring ACLK, but the accuracy is not good so far, so I gonna try your method and set up two timers...
Thanks!