For some reason I didn't get your messages over these days so really late reply here.
As far as generating the .res in the test suite. Those were generated using the the test code and just verified using a variety of xml sec tools to insure it was correct, so no magic there.
Not sure if I am following this last question. The validation is completely driven off of the the references you used to generate the signature. The fact that keys are base64 encoded have no bearing on the signature itself as those are really just encodings the keys are transported with. Typically the key sections themselves have attributes indicating this so that they are properly decoded when being used.
Rob