First: The default wav pitch should be in line with the synth's oscillators. It's tuned to an A, which fits with the synth's C. They are technically not on the same pitch, but the default settings are transposed to compensate. Just remember that A = same pitch as the synth.
Second: Forget it. Pokey is useless outside of atonal sounds and effects. Been using Klystrack for a couple years now and I composed many, many songs but I have never ever used the Pokey oscillator because it's just pointless. Plus there's no texture coming out of Pokey that you can't recreate with the synty+wav and a little creativity, and at least that way you're in control of the pitch.
Third: In normal mode, all keys on the keyboard input a value in the sequence editor. "0" inputs pattern 00. "1" inputs pattern 01. "A" inputs pattern 10 and so on and so forth. It's a bit quicker to edit sequences this way, but for any song of decent length and complexity, you'll run out of inputtable patterns (0-9 + A-Z = 36 possible pattern numbers) before you're anywhere near the end of the song. I've switched to AHX edit a long time ago and never looked back.
Fourth: http://n00bstar.blogspot.ca/2013/03/kly … ction.html
Fifth: Options often break between versions. Komet bomb takes a lot of mushrooms and he can't always be trusted around code. Sometimes nobody notices for a few versions, especially for weird rarely-used options like the multiplexer. The multiplexer might have been broken for 20 versions for all anybody knows. I never switch to a new version (because there's no backwards compatibility for the song files.. so you can't load a 1276 song if you're using the 1275 build) until I am satisfied that all the options I need are functional, and that there are no new options/bugs that will make me want to choke a cute bunny.
Sixth: Welcome to Klystrack, here's your membership card and complimentary tank top. Meetings are every other sunday at the community center (bring food). Updates are once a year, when Komet realizes he's been ignoring us for almost twelve months and feels bad about it, usually around Christmas. Our theory is that he is visited by The Ghosts Of Code Past, Present and Future and he gets Disney'd into doing good deeds. Either that or aliens. Who cares...updates!
I've shown the code to many people, and none of them want to touch it with a ten foot pole...so you're going to have to compile the player yourself and included in the pack! I'm sure you can script that somewhere in your stuff 
