What exactly is the issue?  If each rom screen must be placed in a folder named after the rom with the screen named 00001.png, it would be trivial to whip up a program to rename them.  Here's an example to see if I understand this right:
GENESIS ROMS 
==========
3 ninjas kick back (u) [!].bin --> 3 ninjas kick back (u) [!]\00001.png
36 great holes starring fred couples 32x (ju) [!].bin --> 36 great holes starring fred couples 32x (ju) [!]\00001.png
688 attack sub (u) [!].bin --> 688 attack sub (u) [!].bin\00001.png
addams family, the (ue) [!].bin --> addams family, the (ue) [!].bin\3.png
...
Anyway, if that's the problem, I can make a program.  If it's not, which seems likely, let me know what the proper format is, and I'll see what I can do. 
I gotta say though, what were the creators of this system thinking?  Perhaps they don't have large rom collections.