Did infections (particularly fungal) get worse for ectotherms as endotherms evolved?

I'm not sure exactly what your question is here, but I'm pretty sure that no one could answer many questions about infections in creatures that ancient. I think you are asking if the evolution of warm-blooded creatures somehow made their cold-blooded cousins more susceptable to infectious disease.

If I were to speak very generally,  I could say that while occasionally pathogens do cause mass sickness and even death, for the vast majority of the time pathogens and host organism are in a constant co-evolutionary stand-off where there is little or even no disease except for what we term "opportunistic" infections; open wounds, weakened host through hunger, impaired immune system. So to some extent we evolve in tandem with our diseases, called co-evolution.

One thing we can say is that pathogenic organisms are often quite specific, especially animal viruses, with only rare (but significant) examples of cross species transmission. Bacteria and fungi are less fussy for a place to live, but to grow optimally they need a fairly narrow temperature and humidity range. So, as a general rule, species of pathogen (be it virus, fungus or bacterium) that might infect an endothermic creature would be much less well suited to infecting another animal who lives at different temperature. My guess is that existence of one probably would not directly cause the other to have increased disease, except in exceptional circumstances.

Sorry I could not be more specific, you questions is very broad