I love this forum
I manged to fix the aiming with the patcher. The torpedo guy with his perks was indeed the issue. The patcher has an option for disabling the speed bonus for torps. The best part is that I worked straight out of the box. Didn't need to start over from the base. I reloaded last night's save and I managed to hit the ship with pin-point accuracy.
Thanks for the help guys, I really appreciate it.