The low pedal would seem to indicate air in the system, or a failure of some sort in the master cylinder. You could be leaking fluid around the internal seals on the piston for the rear brakes, which would cause excessive pedal travel and essentially little to no rear brakes since you're not generating pressure in that brake circuit. Fluid will still bleed, albeit probably not with as much pressure as it did before.
You can check the master cylinder by essentially performing a plugged-port bench bleed (on the truck or the bench), where you plug both outlet ports and then stroke the pistons until there's no air in the unit and it hydraulically locks. By disconnecting the brakes from the MC, you isolate the unit so there aren't any other variables in the system. Since your MC has been in use for a couple of years without issue, it should in theory already be bled and hydraulically lock pretty much right away, aside from whatever air you introduce into the outlet ports when installing the inverted flare plug fittings. If there is no air in the MC and the pistons still travel in the bore (slowly or quickly) when apply force to the piston, then the unit is passing fluid internally around the seals which is returning fluid up into the MC, thus little to no pressure in one or both of the brake circuits. While you don't know necessarily which seals internally are leaking, you do know that you need either a new master cylinder or a rebuild kit for the one you have. IIRC, Wilwood doesn't sell rebuild kits anymore and requires that you return the units to them to be rebuilt at Wilwood by their techs.
Tobin