You can generate IR for the declarations while you're transforming it.
Once you've loaded the
.bc into a Module, you can call
module->getOrInsertFunction("pthread_XXX", etc.). As long as
you don't add any BasicBlocks to it, it's a declaration. Just create
calls to it where needed.
As soon as you're finished modifying the Module, write it out with the
BitcodeWriter.
Or wrap your transformer up in a Pass and just add the declarations to
the module in your pass init and insert calls to them in your
handlers.
Hopefully, your transformer won't have to even look at the C source.