Finally on Monday, after much cursing I figured it out the problem after comparing basically every internal signal in the Simulink model to what it should be using lsim. It turns out that the multi-channel transfer function block I was using in the LTI controller was spitting out garbage. Fixing this involved copying the little fucker from a working diagram I received from my advisor. What was maddening was that both blocks implemented the identical transfer function...at least identical algebraically.
Now, I had to use this custom block because Mathworks, in their infinite, overpriced wisdom, doesn't have a transfer function Simulink block that works with multiple channels to my knowledge. Our lab created this one to use, but unbeknownst to me it assumes the denominator is monic, which wasn't the case in the block I was using. This is what I get for using software without really knowing the details under the hood.
Anyway, shits sort of working now with multiple channels in the experiment, just meeting my little deadline. Saturation's the enemy now, but I think I can fix that with the forthcoming hardware mods. There's still a paper deadline in a couple weeks though that I'm going to try for.
