Yes the front of the tank is lifted a 1/2 inch for the stacks. The right side fits fine though.
I think the slot in the left side cover that the tank fits in needs to be ground-out to be larger. I can't get it to fit even with the mounting bolt removed.
IMHO if the frame mounting bolt is completely removed, you should be able to fit the top portion much better than you have until now.
Another possibility ... if your fuel tank is raised 1/2 inch, I believe that there would be a gap on each side ... but you don't on one of the sides. This tells me that the fuel tank might not level (from left to right), or that the side covers are very rough (which certainly could be).
Note: There was a gap on each side of mine (I/S fuel tank ... raised 1/2 inch).
Hope this helps.