That photo is a 68 and wont' do ya much good because 69 is different...I don't believe you have a circuit breaker on the firewall as shown in that pic.
20 amp fuses sound too small to me. I don't know what amperage that motor draws, but it has to be quite a bit. This might be a simple matter of someone putting a 20 amp fuse where a bigger one belongs. Doesn't your fuse box have printing on it for each slot suggesting the correct fuse size? My 68 does...
Yes I'm asking about the wire size going to the motor...red/green sounds correct. If you simply confirm wire size, you can use standard electrical amperage ratings for wire size, and make sure you put in a bigger fuse, but one that will not be so big as to allow the wire to heat up and melt.
As for wiring diagram, I know in my 1968 Service Manual the convertible circuit is not on the main pages with the rest of the large wiring diagrams. It's a tiny little diagram that's labeled "accessory circuits" or similar and is in a slightly different portion of the book. Not sure how 69 Service Manuals are laid out, but I can't believe that Pontiac left it out completely. Presumably you have a complete 69 Service manual you are referring to? It's gotta be in there somewhere...
As for left kick panel, my 68 is also equipped with power windows. I found some circuit breakers under the left kick panel tucked up in there somewhere...probably for my power windows. I was just guessing MAYBE they stuffed the 69's breaker for convertible top in there too. If it exists. I'm TOTALLY guessing...again I don't own a 69 so maybe I should just stop trying to guess...
It just seems this site doesn't get much traffic anymore. I find it hard to believe nobody around here with 69 Convertible understands exactly where/how this circuit is set up...it's gotta be pretty darn simple...switch, protection device, wires, and pump. Not sure what more there could be...