Manual trans needs to be in Neutral when you remove and install shifter, otherwise you will get what you described.
You need to pull out the shifter again and manually align the two rails to neutral, then install the shifter
Last picture in this article shows trans rails in neutral position: TRS Magazine - Shifter Bushing Replacement
You can see the two slots aligned.
You may need to rock the truck(move the drive line) to free up the rails to move them as they can be locked from pressure.