I just got a gsr trans and the case is broke where you bolt the t bracket at need to the speedo would it be safe to still run it with 2 bolts in it or switch the case since I have a spare ls case

 

Might be able to get by, I wouldn't though. Switch the case. Be sure to shim the mainshaft and diff.

 

Do I have to change the bearing and how do you shim it I have the case off a trans but never got to rebuild or change anything

 

You will need a Helms manual and a few specialty tools from Honda (for the mainshaft). What style diff bearings does the GSR have?

 

I have not opened it yet but I pulled the axle seals looks like its not the same as the ls

 

Here are the numbers from http://www.hondapartsunlimited.com/

Another possible option is a used trans.

 

The cases are the same.

I would have the internals swapped over by someone that has experience doing so and has the proper tools. Much better route knowing what you actually have than taking a chance on a used trans.