Possible to use timer1 interrupt with 3 PWMs?

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i using pwm on pins 9, 10, , 11 control small gear motors single mosfet choppers.  that part works ok.  but depending on load 2 of motors slow down or stall (the 3rd 1 lightly loaded works fine) want add feedback.  i adding led/phototransistor hole in gear signal.  my question using timer while using pwm.  i haven't modifed frequencies (even though little higher good).  what 1 ms interrupt can count time between edges (using variables not using internal counter registers).  the bike speedometer here:
http://www.instructables.com/id/arduino-timer-interrupts/?allsteps

looks way  and speed/time range looks ok not sure if can use timer interrupt while using pwm.  since haven't modified timers pwm can still use 1 khz interrupt?  i need monitor 2 sensors additional variables , inputs @ each interrupt.

this on uno board.



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