Ant way to retain brake wear warning and use aftermarket pads with stock system? Also
 

do I need to replace fronts (not worn) if I am putting on HPS on the rears? ABS / braking issues with dissimaler pads??

you need to buy a pad that has a wear sensor to use the stock system, although
 

there aren't a lot out there that have it. You don't need to replace the front just because you're changing the rears, AFAIK. Typically the fronts wear a lot faster than the rears. I would change pads a bit before the wear sensor come on though.

With aftermarket pads....drill the pad, insert the wires from the sensor harness
 

epoxy with hi-temp epoxy.

ECS Tuning has instructions...go to step 7 of The Stage III brake kit install...<ul><li><a href="http://www.ecstuning.com/stage/support/docs-B5S4-Braking-Stage3.html">Check here...</a></li></ul>