I've not played in a "combo" league before, but aren't you required to keep the combinations at 5.5 or below? If you played two 3.0's together that would be a 6.0 team, which would be above the limit. Seems like you'd always have to mix the weaker players with the stronger ones.
Also, and I'm not trying to nit-pick, but I don't see how you can comply with not stacking if you don't play your best team at #1.
Based on what you said, if it was me I'd probably just come up with a schedule that included everyone the required matches, and mixed people around with different partners unless two people were adament about playing together. To avoid "stacking" and to avoid being too predictable so that your opponent can stack against you, I'd just randomly choose who plays on which court.
But, maybe I'm all wet.