Hi Sean;
If the low pedal developed slowly - so that it was hard to notice until it got bad - you may have a stuck caliper piston on the rear axle. I repaired a bunch of them over the years. What happens is the stuck piston supports the pad and as it wears the moving piston distorts the rotor over further and further to make the "pinch". That distortion makes for a slightly mushy pedal. Pull the rear wheels, and have someone pump the brakes, with the engine running to get the booster going, and look at the pads. If they move enough that you can see them move, then check for a stuck piston. The Ate calipers have a bad habit of seizing a piston. It's worth a try.
Rhys