Then you are in neutral.
Let me step back. This is what I picture. You have the case halves together. So you put the crank and the tranny back in - you put the shift forks and pins in the tranny, then the case halves and bolted it up. Now you are staring a motor with no flywheel, no clutch, etc. You are putting the shifter on the shift shaft and trying to get the bike in gear? Am I understanding? If so you need to put rest of the shifting drum together - meaning, connect the DRUM (that is inside the tranny, connected to the shift forks) to the shift shaft (the foot selector that slide through the clutch side). Do I have the clear picture? If not, explain again I'll try to get it.