atmega32u4 use Timer as souce for a counter
There is no way around it, you need the external link.



The only other way to do it is to use Timer 4 to generate your clock. One of the outputs of Timer 4 shares a pin with the T1 pin, so theoretically you could set Timer 4 up to toggle the output pin, and Timer 1 to use the T1 pin as its source and save an IO pin in the process.

The pin would have to be configured as an output in order for Timer 4 to generate the clock, however this is not an issue. Even in the Tx pins are configured as outputs, they can still clock the internal timers:


  If external pin modes are used for the Timer/Countern, transitions on the Tn pin will clock the counter even if the
  pin is configured as an output.


(Extract from Datasheet, P134)