I would probably guess that perhaps you don’t have your NTA (notes to arranger) channel from the keyboard set to control the harmonizer correctly. In theory at least, the harmonizer wants to hear simply the notes that determine the chord you are playing, which is why they work so well with a guitar input.

You might want to take a closer look at how you have the TC set to receive MIDI, it should be decent tracking without audio ins…

If you are losing one side of your stereo mix to controlling the TC, perhaps your mixer has a spare ‘send’ or monitor output that you can use to send to the TC so you aren’t losing half your mix. AFAIK, there’s no way to have both outputs of a stereo output send the exact same thing. Yes, you might have all the instruments and kits panned centrally, but there are a lot of sounds and ALL the kits with distinct left and right side sounds (say a drumkit’s Tom toms going left to right) and the effects like reverb’s phasers and especially panners need both sides to sound the way they’re intended. Even if you run mono, you need both sides…

If you can’t get the harmonizer to work with MIDI alone, try using a mixer send…