I'm not a hardware specialist. I think some-one else can answer this question better than me.
Because pin 3 and 5 are not used, it seems OK to use pin 4 and 6 as support.
If I understand it good, pin 1 is an input. Pin 2 is the output of pin 1 , and connected to 9, 11 and 13 (input).
Pin 8, 10 and 12 are 'output' and needs to be connected to the resistors.
I see that the 'external' wires are not connected as written in the doc.
The cut trace, as shown on your photo is, is needed for a 74F08.
Maybe, the former owner tried the first clockpatch, and then he replaced it with the other one.
The clockpatch looks wrong, but again, I'm not specialist for that.
Werner Frey made a universal clockpatch, on a separate board.
Look at his website http://www.frey-d.de/werner/atari/atari.htm
You can download the schema's, and make the board with jumper yourself.