My IMAC Extra setup (in Avatar) is pretty much stock-basic-no frills. 9303 - AR9000 - two remotes. My linkages are exactly identical in length. Two regulated fromeco 2700's through separate switches to the RX. Deflections were set up using a digital deflection gauge. There is no visual discrepancy between my elevators and no tracking issues in flight.
I think checking the amp draw is an excellent idea. I did that when setting up my ailerons. Your hinges might have slightly more drag on one side than the other. The nice thing about c-arf pocketed hinges is they have essentially NO friction. Back to the battery... I personally would never fly a 50cc on one battery and especially not one nimh pack. They have a poor track record with me. I recently lost my 8' telemaster camera plane because the 1800 nimh 5 cell pack couldn't provide the power.
Checked before the flight under load and it was FINE. Nimh cells are funny sometimes. They will false peak if you charge them too fast, they tend to have high internal resistance etc etc. I'd really really consider the power system to be suspect. Just cause the battery is in the packaged doesn't mean it wasn't over 2-4 years old from the point of manufacture.