Well I am not sure just what you have done but there shouldn't be a problem getting everything back in place. I THINK you are stating that you have the entire top of the transmission off, which means you have the floor open.
If you were shifting (pushing) the forks and not using the stick, you have positioned one so that the interlock isn't allowing you to then move the stick. You will have to get all the forks in their neutral position. When you do that, the stick will move side to side. You may not be aware of the interlock. There is a ball check, detent mechanism which will allow the transmission to be in only one gear. That is, after you have put the transmission in gear,(any gear) the interlock precludes/disallows the movement of the other fork rails. So at this time, the only rail that will move is the one that needs to.
Shift the forks to neutral. That will require the center section where the lower end of the shift lever rest to all be aligned. Then set the shift collars at each of the fork positions so that the transmission will be out of gear. (They probably already are) The shifter can then be put in place and it should drop into the correct position.
Once you get the forks in neutral position, you should be able to wiggle the other parts into place without a problem.
If that won't correct it, I haven't a clue.
James