For the intakes, the outer walls interfere with the fuselage halves, so they rotate out of alignment. The vee splitter on the fuselage on the left side also needs to be trimmed so the intake can seat tightly to the fuselage.
If your gun blanking inserts fit with no step, then you are lucky. All four inserts in my kit were shorter in height compared to the fuselage cutouts.
The tail cone issue is caused by sink marks from the internal bulkhead and I think there is a tooling error where the cone and fuselage do not have the same contour.
Interesting that Eduard caught the trailing edge detail.
Still, it’s a lovely kit. I hope Hasegawa do a AJ-37 Viggen eventually. I was not wowed by the Tarangus kit.