If the horizontal stabilzer is only a little bit out of alignment it'll fly ok, although it may want to veer one direction. You should be able to correct that with your aileron trim. For your motor, aligned to the left is going to make it want to pull to the left. Once again, corrected with trim. However, there is a simple solution for the motor. Simply place washers under the left side mounts for the motor, which will cant it back towards the right. Motors/engines on planes are usually built with a little right thrust into them to correct for left thrust caused by the torque of the spinning engine/motor. So you'll want to get some right thrust into it if you can. If not, try to get it as close to center as you can.

Ken