alignment bolt problem
 

So im a complete newbie to transmissions and im making my first attempt at rebuilding a t56 and every thing was going smooth right up til I got to the torx alignment bolts. Iv done a bunch of searching but not quite finding what im looking for. Every time i put the bolt in for the shift rail it keeps pushing the shift rail backwards, do i need to take the main case off and go back and adjust again or do I need to just keep moving the rail up til I get the alignment right? Thanks in advance for any help.

Thanks for the help. Its finished now.