I never tested this and it is a bit of a Frankenstein approach, but maybe unplug the emitter from the MRF-350. Add a Y adapter and two 3.5mm M/M, both from the Y adapter and one to the MRF-350 and the other to the GT IP2IR. You may need to adjust the output levels after this.

Honestly, it seems you would only be causing more issues than gaining anything, but that is just my 2 cents. You could always call a pro to upgrade your MRF-350 to a MRX-2 (with a RFX-250) and pay for the iPad URC app.

EDIT: Listen to Lowhz over me. I am not a pro. I did not see his post prior to mine.