Purpose of the logic gate configurations on the Kenbak-1
The Flip Flop divides the clock by two, and makes a perfect 50% duty cycle clock.
I think the NANDs are surplus in already available packages on the board, so why not use them if they are fit for the job? They may also function as a fan out buffer (increase output current).
The NOT2 inverter looks like it is an open collector (in contrast to the NAND) type with a pull up resistor. 
Unsure why the diode is there.


Part numbers may support this theory.