Shaun,
Here's one way of making sure the alignment is correct. Stick a plug in each end of the bypass tube and another in the pipe exit. Connect them with a threaded rod on center. This will make sure the bypass and pipe are aligned. Then, drill the bypass tube for the straps, and attach the pipe to the bypass tube without disturbing the alignment.
Remove the threaded rod, and install the bypass and pipe into the airframe. Recheck the alignment optically. Install the engine. Eyeball it again from the rear.
This doesn't take very long to accomplish, and will ensure alignment.

Use a hat section between the mount straps to center the engine in the tube (on the bottom). This will also prevent the engine from sagging downward in the event of a hard landing.