I decided to charge the bike normally with the stock firmware to see what would happen. The batteries charged ok, but fell short of a full charge.
I decided to reset the battery meter to tell the bike to keep charging, but decided to go ahead and upload the new firmware... Well, that did not go as expected. I clicked on the directory and the program crashed, I tried various things and both versions of the software. I couldn't get the bike to start charging, the charger firmware program was corrupted in the process. I pulled the cords and turned it all off, I should have left the bike on until I resolved the problem, less chance of bricking the charger.
The following day I messed around with the program without the bike connected and found if I entered the location of the file instread of the browse feature it didn't crash the program.
Back at the bike, hooked it all up, told the program where to find the file and Viola! changed the charger firmware to keep the lithium batteries happy and charged.
The new firmware changed the guages a little, no longer have the bar graph fuel guage and have a voltmeter instead of estimated range indicator, both didn't really help too much with the new batteries. The cycle analyst keeps track of amphours and voltages.