Hopefully you have been able to get the clutch disc to separate from the transmission input shaft.With the clutch disc hanging up on the input shaft it must have been difficult to get gears. Try removing the flywheel to pressure plate bolts, it may be possible to get access to these by rotating the the crankshaft using the crank pulley bolt. I forget if that engine has a pilot bearing in the end of the crankshaft. Perhaps the pilot bearing has seized and the input shaft nose is stuck in the bearing.
OK - this is a confusing clutch assembly but the answer is simple. On top of the trans where the clutch slave cylinder mounts is a stright bar that is bolted to the shaft that is in fact the pilot bearing (throw out bearing) fork. Loosen the nut and remove the bar, if you do this after you unbolted the trans there will be a load on it. Use a rubber mallot and tap it until it pops off. This will release the pressure on the pilot bearing. DO NOT WORRY about what angle the bar is at - it is a keyed spline and can only go back on one way. When you reassemble, set the bar AFTER you bolt the trans back in place this way the pre-load of the clutch will force the shaft to a position where it will EASILY drop in place; the bar will turn about 3 degrees back and forth. If you are concerned about the position use a dab of paint on threads and bar after you remove nut. ALSO REMMEMBER when reassembling to place fork shaft in tabs of pilot bearing before you re-mount. Align trans input shaft and pressure plate spline. Just did an '06 Spectra5 and we pryed and pryed to loosen trans from engine block then we realized this is a "push" bearing and you must release this fork since the pilot bearing snaps into pressure plate when you put the two units togeather. Hope this helps someone from spending HOURS and HOURS to figure this out!