My Sd's rear wheel has the wheel weights on the outer edge of the rim on both left and right, but my weights are set 90 degrees apart on the left side versus the right.

If that's how it balances, that's how it balances ... Did you take the wheel off the bike and have it's balance checked?

No, but in about 1000 miles I'll be putting new tyres on. I mount and balance myself. I have a static balancer, so I really doubt it will have me mounting weights at 90 degree angles from one another. I've have never seen that. Just after my clutch cover casting issues, was hoping the balancing isn't a sign of poor wheel casting issues.