Why not just leave the existing casing and jambs and buy a new door slab? You may have to rout or chisel for the existing hinge pattern on the new door. You then would be able to cut the bottom of the new door to size making sure you measure from the bottom up.
Seems like anytime you replace an existing opening with a prehung door problems arise with out of square openings or not enough room as you are dealing with.
I would try a local door supply company or lumber yard.
Just my thought.
2X!
I am doing this exact thing for my front door.
My wife wants a door with a window in it (current door is a solid 6 raised panel door) to let in more light to the front hallway, and I didn't want to go thru the hassles of ripping out all the old door jambs, all the trim and the threshold.
I just wanted a door slab that was not pre-drilled for the door knob and deadbolt, and that also was solid wood with a 6 pain window in it.
That ended up being quite a challenge in itself!
Most places sell the doors pre-hung and they are quite expensive.
I finally found a Jeldwen door slab at Home Depot that fit the bill. Here is the one I bought:
This door is a 36 x 80 size. The nice thing about this door slab is that it has a two raised panels in it, so it still matches my existing back door and door to the garage. It will only take a tiny bit of trimming on the bottom and sides of the door to get it to fit into the existing opening, and I can drill out the doorknob and deadbolt holes to match the existing doorjamb.
It will probably take just as much time to prep this door and install it as it would to do a pre-hung door, but with a slab I don't have to remove and repaint all the trim, especially around the inside of the door since I don't have any of that paint left!
Jim