We have the same filter (on my 10G) and I chuckled to myself when I saw yours because I know how you got that "extra intake" portion to fit. I did the same thing, but now I want shrimp, so I took it off.
I don't think you will be getting any CO2 to make it back into the tank due to the Biowheel. The surface agitation on the outlet will likely degass all of the CO2. I recommend moving the CO2 line.
As for a diffuser I use a Rhinox 1000 and it works with my DIY. I have heard of many other diffusers that do not, but I have pics proving the Rhinox 1000 does.
My journal if you want to see the diffuser at work:
Looks like an awesome start, now just pack it with plants.