The problem continues....
Everything seemed fine for a while, then at some point the flickering brake lights started again but only every once in a while. This time I also have had one instance of a Charging System Failure.
Back in the beginning when it originally started I remembered reading somewhere about the sensor on the negative battery cable being a possible suspect in a similar problem but I failed to ever really look at it. Well I did this time and this is what I found.....
I guess it wore away just from rubbing on top of the battery....
Until I can get the new sensor and put it on I wrapped it up in tape but I was thinking it may have been better to cover the opening with some sort of caulking.