We have a well with heavy iron. We have a water softener, but still the toilets will get bad looking even though we have a whole house filter, in addition to the softener.
My tips, just from my experience.
Because of septic, read the containers of all toilet cleaners to see if they are septic safe. I use Lysol most of the time, and am as happy with the results as anything else I've tried.
I don't know how often you clean toilets, but I don't like to use a chemical cleaner more than once a week if I can help it (because of the septic). I brush the bowl each day, and sanitize the seats, rims etc. with Clorox wipes. I think that brushing the bowl each day, just with plain water, helps keep hard water and iron from building up/staining the bowl, but doesn't dump a lot of chemicals into your system. Vinegar is supposed to be a disinfectant, so if it makes you feel better, perhaps using vinegar between chemical cleanings will work.
Sometimes I think hard water stains just are impossible to get out of toilets, especially if they are old (ours were installed in 1973) and they just don't come totally clean.
I have tried emptying the bowl of water and using Bio Cleaner sold here at Q, and that is the most clean I can get those stains. It doesn't get it all, and takes a lot of elbow grease too, but it is the best thing I've found that isn't harsh chemical.
I think the daily brushing well in the bowl and under the rim will help with build up in general, and there is probably no substitute for doing so daily. And use a good bristled brush, and replace often if needed.
Hope something here helps.
And what kind of results are you getting with the comet, vinegar and borax? I haven't tried borax but have tried the others without much luck.
@goldensrbest