Controlling the base of a N-Channel MOSFET on the high side of a circuit
1) Is the voltage potential between the bases when Q3 is saturated even an issue?


The Q3 circuit is unsafe and too slow.

Please consider instead making Q3 into a current source; place a 1 kOhm resistor in series with the emitter. Then when CLK1 is high, the current through R2 is well defined (5 mA), regardless of supply voltage and of what the MOSFET is doing at the time. The gate drive will be a reliable copy of the square wave on CLK1. Since Q3 does not saturate, the circuit will be faster.


  2) Does the presence of R4 limit the switching speed of the circuit?


Yes, of course. But the rest of the driver circuit is much slower, so I doubt that R4 at 10 Ohm makes any difference.


  3) Should I just replace the transistor Q3 with an optocoupler?


That would have been ideal if the switching speed had been very low (&lt; 1 kHz). At 10 KHz, no, not a standard opto-isolator. You'd need a high speed isolator (opto, capacitive or magnetic).

Also, if the duty cycle is never 100 %, consider a gate transformer.