I apologize if you are well aware of this but offer it hoping it might help...
Exhaust systems often do not align properly unless the various components are all installed but with all the fittings left loose. Then, gradually tightening and, at the same time some slight adjusting during the tightening process will ultimately achieve proper alignment. Sometimes the alignment/tightening process will have to be "out of order" from the manual and/or logic!
My 400 has the DSS exhaust. It was installed by a shop for the previous owner. Since I didn't install it I can't say anything about how difficult it may have been to install but it appears perfectly aligned. Of course, one issue that can arise nowadays is that DSS (or anyone else) is selling exhausts made by whoever they can get them from. Suppliers and their "accuracy" can change, affecting the ease of fitting though I would EXPECT (hope?) that any supplier's exhaust system would be able to be adjusted to fit the target moto properly during install.
In any case, good luck with a quick and easy resolution!