I'll second allowing the spare tire well to be cut out- it doesn't cost anything and allows easier and faster access (and less labor $$$ when paying someone to do the work) when clutch/flywheel/trans service is needed.
I don't have any data to back me up but it is difficult to imagine anything more than a theoretical advantage as far as aero goes for a late vs early tank.
More experienced guys: correct me if I'm wrong, but I don't believe anyone tested a late tank car w/o a spare tire well and an early tank car with a spare tire well and determined that they were equal in terms of drag.
Disclosure: I have an early car with the spare tire well partially cut out and sheet aluminum replacement to keep the profile. Due to my accountant-level fabrication skills it works great as a scoop to collect every blade of grass and spec of dust when I go off road and deposit it in the cabin
I also like the decal package idea- it would make the cars in the series more easily recognizable and uniform.