A little too tired to parse through most of this right now, but I'll add one thought-- you can generally tell normal cracks by the defacing of titles or intros or even the addition of a trainer.
Cleanly cracked won't be obvious. I'm not even sure there's anyone in the C64 community looking into revisiting those old disks like 4AM is for Apple stuff, so I guess that's not really something to worry about yet.
I plan to look into modifying the C64 softlist files soon (probably in the morning, in fact)-- the general plan is to start by moving everything in the existing disk softlist (c64_flop.xml) into c64_flop_misc.xml and add support for other softlists similar to how I did the Apple split. That'll open things up for you to start work.
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Try checking the MAME manual at http://docs.mamedev.org
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