Yes, the environment can be quite daunting...
First, read from page 224 on in the LP& Reference Manual. Not a lot of help, but at least you get the idea of the TRANSFORMER 🙂, which is going to be the one doing the task at hand for you.
Basically what you need to do, is put a transformer object in between your physical input and your sequencer input objects in your environment. Next, you tell the transformer object to change the MIDI information from "Incoming: sustain pedal" to "Outgoing: note on".
If you intend to work like this often, save it in a template, so you can use it immediately when you start working on new songs.
Hoping these links are not outdated, there is more information about the environment found here:
http://www.swiftkick.com/logtoolkit.html
http://www.macupdate.com/info.php/id/10541
Good luck cabling 🙂
P.S.: For a list of MIDI controller values visit:
http://www.indiana.edu/~emusic/cntrlnumb.html