Check the Slave Cylinder bolts. there are 2 13mm bolts that hold the cylinder to the transmission.
The cylinder pushes a lever in the Bell Housing which slides the Throw out bearing against the Pressure Plate fingers. pressure against these fingers seperates (disingauges) the PP from the Clutch Disk and Fly Wheel.
something in this area could have broken etc... there is no window or door to take a look
Check the Clutch Peddle operation with a flash light to see if verything is all connected. maybe something came loose. there are 2 bolts that bolt the Master cylinder to the assembly. then the rod that slided in/out of the MC, it is bolted the the Clutch lever. check it for tightness.
the shifter rods to the transmission wouldn`t have anything to do with the peddle not going all the way down.
probably something simple. though I did have the Clutch Disk break 2 of the 6 springs in the center after it was in for 22K miles.
Charlie