That ball is such a pesky little thing. They'll hit the floor and fly all over the place and you'll never see them again.
The order is (if you are looking from the clutch side) long straight rod, ball in the middle, and then shorter rod with the threads on it. If you put it in in any other order, remove it and reinstall.
You can force the rod and ball out if they're able to come out by removing the clutch paddle arm and hitting the hole it comes out of with compressed air. That forces pressurized air through the center of the input shaft. If they're in there and not completely jammed, they'll pop out then!
If you have lost the ball (but have both the rods in good shape) no worries! You DO have to replace the ball but you do NOT have to spend big bucks or wait a long time to do it. You can go to a local hardware store and ask about hardened ball bearings. 3/16" ball bearing is what you need (not the .177" BB out of a BB gun but a true chrome coated hardened ball bearing) to go between those shafts.