My saturn sl2 is shifting hard on his bad days

check to see if the catalist inside the exhaust is rattling around restrickting the exhaust flow

that means your rings, valves, or head gasket are going bad beyond the normal aging of all the cylinders. the number 3 was the first to go on my 91 DOHC too. the car is nearly 20, and that stuff happens with age and use. I would look around for a low mileage DOHC Saturn engine from a 94 SC2 or SL2. the engine is so old that to fix it you will have to rebuild it which will cost far more than the 500 dollars the whole car is worth. the same engine was in them from 92-94, possibly even a 95. make darn sure you find a DOHC engine and not the SOHC, they look almost the same but they are not interchangeable unless you change the transmission, the exhaust, all the wheels, and the speedometer.

It's possible, especially if the used trans sat unused for a while. When you change the filter, make sure that the trans has fresh, proper fluid.

do tune up and clean throttle body see if that helps

It sounds like your hydraulics might have gone bad. They are no longer pressing the pressure plate hard enough in order to disengage the clutch disc from the flywheel.

If the pedal feels any different this may be an indication that the hydraulics are bad. Otherwise it could be the pressure plate fingers are worn enough where it won't have the spring pressure needed to push on the outer diaphragm to disengage the clutch.

Also there is no "oil" in a manual Saturn transmission, it is ATF, the same stuff you put in your automatic transmission.

broken gear in the trans. i hate to tell you but the trans needs to be rebuilt or replaced.

egr valve stuck

well if it shifts very hard into every gear that means the pressure control solenoid in the trans went bad and it causing the trans to go to max line pressure thats why it shifts so hard,,,it does that so you can still drive it even thou it broken,anyhow the PC solenoid is under the trans pan which is on the TOP of the trans under the battery,,,,not too hard a job to do, the parts are about $100 labor might be about $200,,,easy fix,,could be alot more,,,and if you dont fix it ,it will break other stuff in the trans and cost alot more,,,

Saturn says and I quote

there transmission fluid is not to be changed after the first change at 6000 miles.

Now I say it should be changed at every 30000 miles. If changing out the fluid doesn't work then you need to go to a transmission repair shop.

What this code means is the trans is slipping, the most likely cause is internal parts failure or shift solenoid issue for 2nd gear, but based on what I know of this code you will end up getting the trans overhauled.