Is the problem that you want to pedal at different cadences? If your stoker's legs are shorter than yours, and your tandem's cranks are the same length front and rear, then your stoker is being forced to pedal in bigger circles than is natural for her. If she DID use those longish cranks on a solo, she would probably pedal more slowly in a higher gear to compensate - but she can't do that on a tandem, where her pedalling has to follow yours.
So perhaps the solution is to have (e.g.) 172.5mm cranks on the front and 167.5mm cranks on the back. As far as I know, only TA supply cranksets in differing lengths front and rear, and they're not cheap...
As an aside, my stoker and I have tried out-of-phase pedalling with the stoker's pedals three chainring teeth "behind" the captain's, and didn't like it. We found that stopping/unclipping and getting under way were both more difficult. I would imagine that 90-degrees out-of-phaseness would be worse. On the other hand, the experiment is free!