If the original problem was a short on one of the Q1-Q3 then Q6 will probably be dead as well. Change it to the new MPS751 (or similar) instead of MPS2907.
I don't see any reason that Q5 should be damaged from this scenario though. Also, the sidetone comes in much later in the signal path. Maybe Hans can confirm if the Clk0+Clk1 is shut down during transmit so no receive mixing is on during TX thereby deactivating the stuff before R27 pot. Or measure the Clk0+1 pins to see if this is the case.
Scope Clk2 all the way through IC3 and to the gates of Q1-3 to see if they get a signal through, depending on the fault that IC could get +12V on the pin3 output and fail.
DMM to check that the RX/TX switching is working at IC3 pin 12 & 11.