Sounds like a shift motor issue to me. I would pull them and check under the motor casings for carbon dust from the brushes. Failing that, it might be worth checking the harness.
There aren't a lot of components connected to the TCU, a couple of sensors, the clutch actuator, and shift motors. I would think any issue will be found on that short segment of the harness. Perhaps double-check your connectors and ensure everything is securely plugged in.
Edit: If I understand you correctly, you changed the transmission? Did you not disconnect the harness then? The harness starts at the TCU under the driver's seat, passes through the body and into the engine bay behind the drivers seat, and winds it's way around the transmission area to connect to the various components. That section of the harness is maybe 6' long.
There aren't a lot of components connected to the TCU, a couple of sensors, the clutch actuator, and shift motors. I would think any issue will be found on that short segment of the harness. Perhaps double-check your connectors and ensure everything is securely plugged in.
Edit: If I understand you correctly, you changed the transmission? Did you not disconnect the harness then? The harness starts at the TCU under the driver's seat, passes through the body and into the engine bay behind the drivers seat, and winds it's way around the transmission area to connect to the various components. That section of the harness is maybe 6' long.