Annoying transmission problem sc2
 

Ok I recently replaced my 98 sc2s engine with one from a 2001. We put the motor back in, starts up fine. Replaced the 98 clutch and now it will not go into gear once the car is started. So I replaced the master and slave cylinder that was prebled. Popped it in and still the same problem. It just will not go into gear once the car is started. So I guess my question is could there be a problem with the 98 clutch mounting up to the 01 engine in anyway for it to cause this problem?

I can not answer your question from a personal standpoint other than while not swapping an engine on a Saturn and in all honesty avoid the thought of it on a FWD automobile I have swapped engine on many rear wheel drive cars and worked on hydraulic clutches.
It sounds as if the slave cylinder is not working so the clutch is not releasing correctly
This at least raises the question of; are you sure the hydraulic clutch is actually functioning?
Being able to put the car in gear with the engine off is not a function of the clutch working or not. It is not needed.
If you are sure that the hydraulic clutch mechanism is actually working, it is possible that if the clutch disc itself is installed backwards that it could interfere with the operation of the pressure plate thus the clutch.
If you think that you are smart enough to not do something like that
lemme tell you,
so did I!
Wrong!
But never on a Saturn, mine the engine is still good with no problems seemingly on the horizon.
The following web site gives extensive interchange information. There were some differences through the years and is where I would go to research this.
www.saturnwiki.net

Is there any adjustment for the arm that holds the throwout bearing? It seems that the slave is not reaching the arm and if there's an adjustment for it that could be an easy fix