The effectiveness of the TotalRemote adapter depends on the quality of the audio output port/circuit in the device. The Karma should work as I hope it's audio output is of very high quality.
But the usefullness of such a device on an audio player is questionable at best. I saw the original version Griffen had made for the iPod. Making the newer version for PocketPC was a smart move. It can totally replace a Pronto remote. The only reason to use the audio adapter is to make up for the usually poor IR strength of PocketPC's IrDA ports. Some PPC models however (like my HP 2215) has CiR built in though - so no need for an adapter.
And if you take the time to read the website linked you'll see someone say it won't work properly because you can only get a 22KHz signal out... True (out of one channel), but if you use two emitters, one for each channel, each at 22, you're back up to a respectable 44KHz. And that's exactly what the Griffen unit does.
And lastly, it's easy to convert an Ir waveform into a sound file. No need to even learn any of your existing "codes" if you can find something out there on the net in a documented format. Don't ask why I know all this stuff.
Bruno