@PaulRB Is this what you meant? Assuming I can use all 4 of those IC2 pins at once 
Yes that's fine. Physically you are connecting the 2 i²c devices to separate pins, but electrically they are the same pins, they connect back to the same 2 pins on the atmega chip.
Thank you so much, you have no idea how many hours of my day I've spent trying to get my brain around this! I really appreciate your input, as you've helped solve the last two issues with the circuit I can't wait to finally build it tomorrow
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Is it possible you connected the level shifter incorrectly? We can't tell from your diagram because the pins are not labelled.
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Thank you.
Not this one! It has a 3.3V regulator of its own.
I'll post some photos of both boards wired up as soon as I can, it'll be in an hour or so as I'm out of the house right now, thank you for your input though!
Connected as described here?
UNO
AVCC: 5V VCC ← connected to UNO's 5V pin
ASCL: 5V SCL ← UNO's A5 pin
ASDA: 5V SDA ← UNO's A4 pin
AGND: 5V GND ← UNO's GND pin
nunchuk
BVCC: 3V VCC ← connected to UNO's 3.3V pin unconnected
BSCL: 3V SCL ← nunchuk
BSDA: 3V SDA ← nunchuk
BGND: 3V GND ← nunchuk
Yeah I was trying to follow that as it's in the amazon listing description. I did it a few times just to check I hadn't done it wrong, but had no luck sadly
I think that may be incorrect...
As I mentioned above, this level shifter board has its own regulator:
This isn't the exact same board and I can't find a schematic for it. But I think it does not need a connection to the Uno's 3V3 pin.
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I think this may be it.
yes, that looks identical to the one I bought! the connector for the nunchuck has 4 pins too, Clock, data, + and -
I agree! (thanks). The manufacturer's link is misleading ...
The level converter is very easy to use. The board needs to be powered from the two voltages sources (high voltage and low voltage) that your system is using. High voltage (5V for example) to the 'HV' pin, low voltage (3.3V for example) to 'LV', and ground from the system to the 'GND' pin.
Based on this schematic and images, the converter's 3.3V output should be left disconnected.
I've corrected my previous post by striking out this connection.
Should I then attach the ground from the nunchuk board directly to the uno to complete the circuit?
Yes. (you may have just found the real problem) 
I think it should be ok to power the Wii nunchuck, as long as it doesn't draw more than 150mA.
Worth a try, but I doubt it. The bottom layer of the level shifter's PCB looks like it's mostly ground plane and connects the AGND and BGND pins.
If that's true, you didn't connect it properly:
The power and ground wires should be on the outer pins and the I²C lines on the inner pins.
I've gotten home and tried to wire it again, triple checking that my wires are in the right place, but still no luck. I also tried with and without a ground wire back to the Arduino, and just in case, the ground wire between the shifter and nunchuk. I've taken photos of my wiring for the version where neither ground is connected. White is 5V, Black is ground, Blue is data and Purple is Clock. As I'm having so many issues I'm going to try and problem solve with the sparkfun board, as that at least came back with data even if it was wrong.
EDIT: I am no longer using this blue level shifter as I couldn't figure out what was wrong. I am now looking to use the SparkFun level shifter instead, as discussed below
Hi,
Do you have a DMM?
If so can you please check that 3V3 is getting to the nunchuck?
The PCB is connected into the socket the right way around?
Pictures tell a story and unfortunately Fritzy images don't.
Can you please reverse engineer and draw your circuit on paper and post an image?
Include component names and pin labels and power supplies.
If you look at your Fritzy it has no pin names for that level changer, so how were we to know it had a 5V to 3V3 regulator on it, the nunchuck pcb has its pin names obstructed.
Thanks.. Tom.. 
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Hi Tom, I've got one on the way but it won't be here now until mid next week. By PCB and socket, do you mean if the pins I've soldered in are the right way around? It was a second attempt at soldering the board as I accidently damaged the first one with too much solder, so I flipped the board to avoid making the same mistake.
I can just use the sparkfun board level shifter instead, but the data is coming back wrong at the moment, just trying to troubleshoot why if I don't have the tools to fix the smaller board in the diagram. I'll get onto that drawn version in case it helps at all