So I'm just posting an update. I was able to get past the National Treasure mission and progressed to the end of that story chain, but now I'm just still stuck with Radio Libertad, and that is the only thing holding up my progression to finish the story mode. If anyone figures out a way to get around or even skip that mission without the repair tool, please post it.
Do you know if savegames are shareable? We might could edit it somehow and fix the issue causing the lack of progression.
You can play the DLC just fine without invisible and unlimited ammo. I beat it on level 5 already and done all the challenges and achievements. Just use no reload and that takes care of the unlimited ammo, and with infinite health you really don't need invisible.