Regarding the issue of pinholes, I initially thought they were because of the pH change going from developer to acid stop bath, but I still get them occasionally when using just a water stop bath.

I'm of the opinion now that they are primarily a function of temperature change between solutions; I tended not to regulate my tray temperature in my garage-based darkroom for APHS, treating it much like paper. I make sure it's in the ballpark, but don't get serious about temperature regulation like with panchro sheet film. I'm going to change my working methods with APHS to regulate the temperature to a finer degree of control.