strange timing issue

Which tower is which, makes no never mind. As long as the rotor ends up close and the timing mechanisms do not cause a crossfire/missfire,you're good to go. Don't lose any sleep over exactly where the rotor is. On a slanty the factory coil can handle a lil extra rotor to tower gap, and in fact that extra spark-gap will make the coil work harder to deliver more to the plugs. I'd call that a win-win situation.