... I'm going to build a Bassman 6g6-b. ...
Cool! Good luck with the build!
I don't know if your boards came with a schematic, or if you're referencing one. So here's the
Fender 6G6-B Bassman schematic.
Look at your rectifier/bias board (with all the 1N4007 diodes). You're missing a 27kΩ 1w resistor which goes in parallel with the cap on that board (reference the layout; this board is towards the upper-left corner).
On you main filter cap board, you have a green-insulated jumper wire and a pair of 220kΩ resistors connected to the first two 20uF caps. Get rid of those, they're not present in the 6G6-B. I think I know what you were trying to do, but as-is the jumper is shorting high voltage to ground and the 220kΩ's are not in the right places for what you were looking to copy. The main filter board is not shown on the Fender layout (because it was outside the chassis under a metal cover), but the schematic shows these first two 20uF caps connected in parallel. So you will remove the green jumper and replace the 220kΩ resistors with wire.
On that main cap board, you probably also want to connect the - ends of the first two caps to the - ends of the other caps. Or, if you wanted to keep those grounds separate, make sure you install a wire for each set of grounds so you don't have a hard troubleshooting problem by having a missing ground.
On your main fiberboard, I see the 100kΩ plate load resistors for V2, but there are two caps connected to them (with a lead hanging in the air for each?): a silver mica cap to the left in the picture and an orange drop on the right. In the Fender layout, it shows only a single cap (0.002uF or 2000pF) across the 100kΩ which connects to V2 pin 6.
Other than those items, everything looks okay as far as I can see (pics aren't close-up enough to see color codes on resistors to know all values are correct).
... My main concern right now is the cap on the presence pot. Every other build I've seen the capacitor is huge compare to this one. Should I replace it?
Nope.
The schematic and layout says 0.1uF 200v. You cap appears to say 0.1uF, and it really doesn't need a 200v rating. Your cap appears to be metallized polyester, which is a dielectric and construction style which results in more uF's per unit volume. Others might be hung up on using orange drop caps everywhere, and the most commonly-used variety of those is polypropylene film & foil. That dielectric and style of construction makes a cap which is much bigger for the same number of uF's. Often, guys wind up using a 630v cap they have because it's on-hand, even though the presence control circuit will never see more than 50vac under any circumstance. A higher voltage rating also makes the cap bigger for the same number of uF's.