PIT is suited for output compare function only (generate period). I think that it will be difficult to use PIT for measuring of pulse with.
If I understood correctly, your problem with normal timer (ECT) is 2s interval = too long for TCNT timer. Correct?
In attachment you can find simple example code for measuring of pulse width by ECT module. This example code uses overflow interrupt for measuring longer pulses (longer than TCNT period). I suppose that you can simply modify this code for measuring both (0V and 5V) pulses.
You can also simply testing overflow variable for 2s limit in overflow interrupt routine.
Note: There is necessary take into account error of one TCNT period. If you want get better accuracy (of 2s limit), you should calculate with last value of TCx timer/resets TCx timer value….