So after playing with it some more, I've noticed a few things (still doesn't work). The first being that I was looking at the code and the pins didn't really seem to be matching up so I looked at that for a while and realized that all the wiring examples were for SPI, not I2C. Which is fine, I found the SPI library and switched to that. All the pins make sense now, so that is good.
However, I did notice that I had some of the pins wired up backwards. This is what was wrong, and this is how it is now. (the pictures above are not longer accurate for this 1 pin).
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Arduino Pin 3, goes to
NXP 4050 pin 13, which then goes to
NXP 4050 pin 12, which finally goes to
PN532 breakout board pin MOSI/SDA/TX
This is what it looks like now:
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Arduino Pin 3, goes to
NXP 4050 pin 11, which then goes to (notice the change here)
NXP 4050 pin 12, which finally goes to
PN532 breakout board pin MOSI/SDA/TX
Oh, and I checked the continuity of my solder joints to the actual PN532 chip and they were all good. So that eliminates one of my doubts. However, I'm still confused about the jumpers (but even after switching to the SPI library I, again, tried all the combinations I could think of).
Thanks for reading! Any input even if it's just brainstorming is greatly appreciated, cause I'm stumped :/