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I am not quite sure I understand what you are trying to do but I think you are saying that the cases end up being to long and also to thick in the neck area is this correct?
If they end up being to long then you need to aquire the right size neck collect or bushing that will go in your trimmer so that you can center the case and then trim it to the right lenght. I guess if you had to and were careful you could use a file to this but it would crude at best.
Now if the neck is also to thick then you will have to get an inside neck reamer that is the right size so you can ream them out to the right dia.
I do not know if you will be able to find the one you need or not. Years ago I was making .243 brass from .308 cases and I ran into the same problem that you are having. At that time they made a reamer that was made to do exactly what I needed and it worked great but I do not know if one is made for what you need.
Another way that you might be able to do it is to turm the outside of the case thinner on a lathe. Then resize the case through the dies and all might be ok.
Another thought could you trim the lenght of the case back before you fireform it?
One more bit of info for you. Get a hold of the guys at Buffalo Arms. They work with this kind of stuff all the time and they will probably have a solution for you.