A thorny problem. All of your examples, except the first one, appear to be particulate matter on the surface. Do you use a wetting agent such as Photo-Flo? When you hold the film up to a strong light do the spots appear dark? If so it's particulate matter coming from somewhere. How dust free is your drying environment?

If the spots transmit the backlight then the problem is in the emulsion itself. Possibly from dust on the negative during exposure, the lack of "rapping" on the tank to dislodge air bells, an acid stop bath, or QC in the manufacture. In your first example where spots are visible you appear to have an additional problem of fogging, since they are visible in the frame line.

Over the past year I've been using a university darkroom with supplied chemistry. They don't use stop bath for film and from what I can tell this does not cause a problem when arresting development. I've never processed film that way before but I will now, that's one odor to deal with in the process. Oh, to clarify I do use a water fill/agitate/dump procedure for 3 or 4 cycles to stop development, it seems to work fine and you eliminate the CO2 bubble problem when going from an alkaline to acidic environment.