A couple ideas...
Add a heat shield - even if you zero out the ablator. It's still going to bring your CoM down a bit and I think it will help with drag. The bottom of your Service Bay has an open node which is draggy. Adding the heatshield will "cover" that node.
Consider clipping your pod into the top of the service bay so the two have a smooth joint rather than a gap. I'm not sure if it will be different aerodynamically, but it'll lower the CoM. I often think of clipping as cheaty, but in this case you're clipping into empty space, so it seems believable.
Add drogue chutes. They'll slow you down and help the pod orient correctly
Tyko's post in Service bay reentry was marked as the answer