That method of counting pulses absolutely guarantees that you will miss pulses.
You have interrupts turned off most of the time. Yet, you expect to send and receive serial data with interrupts disabled. That is NOT going to happen.
count1 is incremented by the ISR, and used by loop(). Yet, it is not declared volatile, so loop() has no idea that the variable was updated by other code.
Leave interrupts on ALL the time, except for the VERY brief time you make a copy of count1 and reset it to 0.