The is a little tiny shaft coupler inside the transmission that has more than likely sheard off the splines. My MF 1155 did this 3 time before i got rid of it. It connects the front shaft from the flywheel to the rear shaft that turns the pto and charge pump. All 3 time i had to replace the coupler and rear shaft. Just the parts were expensive but getting to it was the nightmare. The transmission has to split right in the middle. Call the mf dealer or abiline machine for help diagnosing the problem to be sure. If it is what i think it is. Abiline machine has the parts much cheaper now. Shaft part # am503433m1
Coupler # am516006m3
Get you a s I&T shop manual from abiline machine too. They are only 31 dollars