I dont know if its an optical allusion. but the box rib profile looks physically taller on the passenger side then the driver side. I wonder if the rib was manufactured a bit off cantered.?
I installed a complete 126 floor pan into my 500, and although the fit was adequate, there is some sloppy mfg on the overall build of the strengthening ribs and the like. Its design is much stronger then the original 500 design, but its unfortunately the way things can be with aftermarket parts to restore these cars.
And yes, typically that flange that was bent over usually stays horizontal. Ideally in that case, i would just cut off the excess bent over flange, to prevent water from being trapped in the u profile.
Would i go about pulling the pans out and redoing them in your case?... honestly it would depend on the interior fitment, finish and such.. The inner sill flange will dictate how deep (up) the floor pan goes. From a glance it seems like nothing is welded in yet?? That horizontal flange on my 500 is excessively long, so i will be trimming it down as i finish the body work. Anything to eliminate a place for water to collect is key.
One last thing, i realize what i say is not an excuse for a properly done job, but just keep in mind, the overall fit and finish of these 500's are not the best. They were an economy car first, and were mass produced at a fast rate. There is a possibly that this fitment issue is compounded by previously replaced parts that were not the best fit also.
Best of luck in getting your 500 back on the road
