Yes, I let it go empty accidentally. It sounds similar. The pedal was really weird feeling; sometimes almost "fluttery", but when it built resistance it would creep down to the floor. If I had not known the history, I would have suspected a bad master cylinder.
I had to cycle it LIKE FREAKIN' CRAZY. Seriously, I just kept running a circle doing one wheel at a time. About the time I thought I wasn't getting anywhere a huge stream of bubble came out of the passenger's right, and it was all improvement from there. I drove it around for a day or two, then did another go around just for the heck of it, brakes are amazing now.
I really used all methods included in this thread; pumping/releasing with the engine on and with it off. Pressing the pedal to the floor, opening a bleeder with the tube submerged in fluid, releasing; Pumping with it open and submerged. Couldn't really tell you which if any of those helped, but the the cycling under pressure seemed to really be the key. Lots and LOTS of cycling under pressure. Well, that and a truckload of persistence; beyond what I thought was reasonable