looking good. man your experiences are so similar to mine last year it's scary, haha. luckily for me, the previous owner had a new diode board installed, and it was beaten into my head before i started working on it to always unhook the negative battery cable (better from the battery rather than always unhooking the vent screw, as people tend to say it strips easily).
not sure what would be spaking from the top, i always have a hard time getting the bottom cables and rubber dohicky in the bottom groove of the cover plate when putting it back on. i guess not getting it in the groove and pinching the cables isn't a good idea. but i can't remember anything on the top of the cover needing any special treatment, but i suppose my diode board is different and situated differently.
the new brake cable is a pain in the butt to get on the master cylinder. i feel like i broke all my fingers until i figured out the best way to squeeze that lever back. having the "official" master cylinder feeler gauge is well worth tracking down if you don't already have it. makes adjustment of the master cylinder much easier.
when i redid my choke assembly i also found it much harder to move the lever, i think it's because i just tightened the nut to far down, as the bolt goes all the way through the assembly from what i remember. might have been easy to actuate since the nut wasn't even on? haha.
i need to get back to my bike and figure out my brake problem! i'm missing some odd nice weather!