Tony,
Not sure if this relates, but I had a customer of mine that put in a new clutch that worked when the engine was off, but wouldn't shift when the engine was on. The problem was that the pressure plate was not the right one for the clutch and there wasn't enough clearance to cause the clutch to disengage when shifting gears with the engine running. You may want to verify that you have the correct replacement clutch. Incorrect or worn throw-out bearings and pilots bearings can sometimes cause this issue also.
If you have the original clutch and pressure plates, there is a place in the Twin Cities that can rebuild them for you. It is Proven Force (formerly Clutch and U-Joint) at 800-444-0755. I usually speak with Bernie or James there.
Ralph in MN
Back to the Home of the AMC Gremlin