1) is that resin stuff harmful to the plumbing (other than clogging the screens on the faucets)
That usually is enough. Is the sand gold colored and feels like ball bearings or slippery?
2) What would cause that resin to come out in the first place? I assume something has broken.
That is the reason.
3) How much would that thing that broke cost to fix and where would I get parts if I can do it myself (I'm handy) (Phx, AZ area)
Kinetico softeners mean Kinetico repair men, (usually expensive repair men). As far as I know they do not sell parts to ANYONE. That is probably the reason it was on bypass.