Step in the fuselage

I find this problem frequently.  I use needle files rather than sandpaper.  They cut much faster than fine sandpaper, but leave smaller scratches than coarser sandpaper.  I think needle files are a neccessary tool for plastic modeling.  They do not last forever, so they will eventually need replacing, but they are not that expensive if you shop carefully.  I get mine from Harbor Freight.

Be carefully to keep the cross section even. It is easy with such a problem to sand or file asymmetrically, making a lopsided cross section.  With military planes with a flat finish, this is usually not that noticable, but with airliners with a gloss white paint on top, it can be noticable.

 If you have to sand or file very much, you may have to rescribe panel lines on the top. but I find sanding or filing to shape just as easy, if not easier, than building up filler on the low side.

There you go.

You could do this .

   Take the model and clamp it in such a way it will re-align under pressure .Then do that as you put more solvent glue on the parts . Has worked in the past for me . But , be careful you don't squeeze it to hard . T.B.

Far be it for me to claim expertise in anything model related,but as I see it you've got three options; seperate the halves and start over,the solvent doesn't help this situation, and try to work the step to the bottom ;or sand away and replicate any details lost in the process,or use some filler and try to fill and feather till you're happy with it. Any and all methods are gonna be messy and time consuming. I'm sure there is a member here who will steer you in a better and proper route than what I think. Good luck,and I'll be looking for pics.