Where the shaft that comes out of the bell housing meets the transmission, there is a cast iron coupler that connects it to the input shaft of the tranny. That coupler has 2 bolts that go all the way through it, and 1 more that only goes into the transmission input shaft. All three need to be removed. Then take a couple of flat screw drivers and drive them into the split on each side of the coupler, right where the long bolts went through. This will spread the coupler and make it easier to slide ahead on the shaft. It doesn't take much, just a couple of taps to drive each screwdriver in. Then just slide the coupler forward on the shaft until it is off the input shaft of the transmission, and you should be all set to pull it out since you already have the PTO shaft pulled.

If you need any more help, don't hesitate to ask.