I suspect the back is causing more drag now. The top already has some relief at the rear compared to the loft apex. A clean bubble can't hurt but look at the rear edges. Two sides and one top. Bottom flow is limited by ground. If you could fair both that could help the wake converge instead of diverge. What's the vertical thing behind the awning leg? If it's cloned on the road side too and permanent then perhaps you could attach their.
Your custom box is very interesting!
