When looking at the docs for the remote that is sold with the unit, that is an RF remote. Did you purchase some other remote in addition to this one to use? I'm curious how you got IR codes into the Pronto from an RF remote. :-)
Have you followed all the instructions about pairing the OEM remote to the lift? i.e. can you use the remote you bought to raise/lower the lift?
[Link: touchstonehomeproducts.com]That being said, the unit is capable of pairing with an IR remote provided you connect the IR sensor to the controller.
Have you tried just creating some codes such as 3 codes for use with for example a Sony CD player and then tried pairing the the unit with the 3 codes you have? There is at least 1 video I found via googling illustrating how to do this for Touchstone units.