Yikes. I see three problems. Front shaft out of phase, rear shaft out of phase, wrong transmission. The first thing I would do is remove the front shaft and leave it off for now. Remove the rear shaft check the joints, replace if needed and re-phase it. Re-install it and drive it. I doubt it will change but its worth trying. The transmission is a 2wd long shaft with a slip yoke. It should have a short tail shaft with a bolt on yoke. The shaft should be with 2 joints and a slip yoke. So doing as I suggested check if it vibrates, If ok by some chance you can check the front shaft joints and re-phase it install and see how that works. Now if it vibrates with just the rear shaft I would try this. Unbolt the transmission shaft from the TC and see if it will slide into the transmission at least 1/2 to 1 inch. If it does not slide the transmission may be loaded against the TC which will vibrate. The motor and transmission would have to be moved forward. Band aide fix and not my choice. What is there is not right and kind of a hack job. If it were mine I would be doing the transmission back to the short style and get the right drive shaft, Right now I will just about bet the problem is between the TC and transmission.