Christ,
Just finished reading through this post. Possibly I missed the reason you wanted to bring this up to a 12 volt system. Was that just to be able to use standard automotive LED's? Also you'd obviously need to toss in a 12 Volt headlight. If you measured the output of your rectifier and it is as high as 8 volts, then the system is probably charging properly.
I bought my wife a cm200t about 18 years ago to learn on and that bike regularly returned 70 mpg with no mods. Now she's riding a Honda 650 that still gets her around 50-60 mpg.
As far as the lithium idea goes, probably not a good one. Lithium cells in general need to be charged within a specific range depending on their particular type of chemical makeup. Some like being charged a little above 4V(per cell), some prefer around 3.6V/cell. A standard charger would probably toast them. However, you might just disconnect the whole charging system, use a couple of Dewalt 36V batteries paralleled up, get a DC to DC converter to step back down to 12 volts and then pull the batteries to charge them in the standard Dewalt charger. Just another possibility.
JJ
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