No, the wire or ends aren't going to change anything. You definitely need to calibrate the system.

You should also move the sub to the LFE input--what the manufacturer recommends doesn't make much sense in modern AV. I doubt it would be affecting the mids and highs, but ya never know. You'll want to play with the position of the M60s as well.

I am the Doctor, and THIS... is my SPOON!