So I did a clutch swap on my 04 rubicon and as I was putting everything back together I noticed my rear drive shaft seemed too short to fit back in, I tried to give it a pull but no luck, any tips?
Pull harder. It will extend. The grease is likely very cold and making things difficult (if you've been having anything close the temps we've been getting).
When removing the driveshaft the slider compresses and when reinstalling the grease seals the splines creating a slight vacuum inside when trying to extend the slider.
IF it's cold outside; find a way to warm up the shaft and it should extend easier.
As above, your driveshaft is likely held in its compressed position by either cold weather stiffening the grease, or that plus a vacuum that forms as you try to pull it back apart. I'd bring the axle inside so it can warm up a bit and try again.