I had the same problem after swapping the clutch out of a 95 trooper, you just have to keep bleeding it. I had my buddy pump it up hold pedal to the floor and then I would open bleeder valve then close it and then repeat. We went trough a big bottle of brake fluid doing this and once no more air came out I had him keep pumping as I watched that rod push the throw out bearing arm and it got better and better. Try this start it up and pump the clutch pedal like a air pump 20 or so times then see if it will go in gear and if it does it just needs to build pressure.