We present comparisons of the spatial distributions of CO, Hα, and 8-micron PAH emission in the merger and radio AGN galaxy NGC 1316 (Fornax A). ALMA CO(2-1) data reveal a highly disturbed molecular medium with gas far from reaching equilibrium during the merger. All of the CO features have associated Hα+[NII] emission, but most of this is weak diffuse emission and not clumpy bright HII regions produced by star formation. There is remarkably little ongoing star formation in the galaxy. The 2 largest and densest gas complexes in the galaxy have ratios of Hα/CO and PAH/CO 10 times lower than the rest of the galaxy ISM, suggesting that denser gas inhibits the production of Hα and PAH emission. Of particular interest is the molecular gas complex apparently interacting with the northern jet at the location where the jet weakens and bends. The ratio of PAH/CO is lowest closest to the jet, indicating that the jet-cloud interaction may be destroying PAHs.