Honestly? Just ditch the whole stock setup. PM a member by the name of awk08. He sells a bolt-on hydraulic rear brake kit which uses a Suzuki GSX-R rear brake caliper. It replaces the cable, caliper, pedal... everything giving you a headache as of now.
Everyone I've talked with loves this conversion kit. I am going to order one myself soon so I can say for sure.
Those stock mechanical rear brake calipers are a joke. They never worked well, even when new.