Q: I'm removing the motor but the input shaft is still in the motor instead of staying in the transmission what do I do?

Hi there. The input shaft is stuck in the pilot bearing on the engine or the back of the crankshaft. If the input shaft came completely off, then you will have to use a slide hammer to remove the input shaft from the engine and then reinstall it into the transmission. If the input shaft is attached to the transmission but the transmission will not come off the engine, then you will have to remove the bolts to the clutch with the transmission mounted and then the engine could be removed. This would be that the input shaft would be stuck in the clutch. You may have to use a torch to heat up the input shaft to remove the clutch from it. If you need further assistance with your transmission input shaft being stuck in the back of the engine, then seek out a professional, such as one from Your Mechanic, to help you.