I figured it out. Turns out all the commands on the original remote, which are detailed in the table, can easily be sent via the RS-232 connection. There's one specific command for doing so which just needs tweaking for each command on the original remote. The "42" code I mentioned above represents the last two characters in the command for the home or "My Apps" button. All the other buttons on the original remote have a similar two digit code. It's really pretty simple once you see it. My TV is now fully controllable via the RS-232 connection so I was able to remove the IR emitter from the front of it.

Most devices that talk via RS-232 only use Tx/Rx/Gnd. On a DB9 connector those are pins 2/3/5. You have a 50/50 chance of getting it wired correctly as some manufacturers use a "straight through" vs others use "null modem". The only difference between the two are that pins 2 and 3 are flipped.