I think the issue is with this:
Now, if I take the output of the Sonic Port and plug it as input into the AudioBox iTwo, not only there's a very high latency, but the sound is coming out with a very strong reverb. It sounds very far away and with a lot of echo.
If I understand this correctly, you're going out of one audio interface and plugging into another. The reason you're hearing a delay is because you're going through two A/D and D/A processes. The reverb effect comes from the microseconds of delay that each device has inherently, because all audio devices have latency.
The signal path is going like this:
Guitar ---> Sonic Port A/D ---> MobilPod on iPad ---> Sonic Port D/A ---> Analog Input to iTwo A/D ----> Computer ---> DAW Monitor through Software ---> Output to iTwo D/A to Headphones or Speakers.
I would expect this entire round trip to take on the upwards of 10 to 20 ms, that is where you're going to hear the reverb effect as it's the input and output of each interface sitting on top of one another. Also depneding on where you have your monitor playback knob set on the iTwo will also have an effect on the monitor.
There's an easier way to do this, and that's not to use the iPad at all.
Why not just get a Pod Plugin for your DAW and do this all on your computer?
You got Studio One 3 that came with your AudioBox i-Two (or the MoiblePod, but not both at the same time), you can use the plug-ins built into Studio One 3 for amp simulation or to expand on it you can get an add-on called Ampire XT that costs less than AmpFarm and use that as your effects stack for your guitar, you will cut your latency in half. Optionally if you absolutely need to have the Pod amp simulations, then you can get the VST support add-on for Studio One 3 Artist and then go get and use AmpFarm from Line 6.
Bottom line you want to reduce the length of time the audio takes from your guitar to the DAW and back. Removing the iPad will let you do that.