I'll note that our fleet of bikes and tandems do not presently include any using a Shimano Octalink or ISIS bottom bracket (we're pretty much square taper city); however, having had a few pass through the livery and having worked on a few bikes that do, I would "think" you could solve the problem by putting an alignment mark on the exposed section of spindle pipe that is visible between the stoker's left-side crank and the bottom bracket shell and/or on both ends of the spindle pipe. You would want to put the mark such that it lines up with under or opposite of the center of the crank arm when installed on the spindle.
A small spot of auto touch-up paint or indelible ink on a freshly cleaned spindle usually does the trick and remains on the spindle for a long time before fading. Moreover, it could be freshed-up when removing the cranks while packing for a trip. You would just need to line up the stoker's timing (left hand) crank with alignment mark on the spindle and then thread-in your crank bolt while making sure the spindle (and spline pattern) remained in alignment until the splines seated.
Anyway, that would be my approach but, again, I'm basing this partially on theory and partially on being anal enough to keep even my square tapers "aligned" with cranks when they are reinstalled by using alignment marks on the spindles.
Last edited by TandemGeek; 03-24-05 at 03:58 PM.