Which is to say, it’s not so much the liberal/left causing a problem here - I think they’re just holding the ground they’ve always had - that vaccines are generally safe and generally a good thing.

Have you read the discussions on vaccine stories? See, for example, https://news.ycombinator.com/item?id=26629234 – chosen arbitrarily using the search box at the bottom of the page. I've not read anyone pretending this.

> shut up

People are being dismissive of you, but nobody has told you to shut up in this thread. (The closest thing is flagging the comments which started with broad-spectrum insults, but this only occurred after you wrote this.) Despite its tone, I'm going to have to second GP's assessment that you're responding to imagined slights.

But you've got to weigh those risks against the risk of dragging our feet on rolling out new vaccines. It's likely that many autoimmune diseases are caused by pathogens which are either undiscovered, or which are known, but whose link to the autoimmune disease is undiscovered. This is because there is evolutionary pressure encouraging pathogens to resemble self-antigens. If a pathogen has markers that cause it to resemble the human liver, the human adaptive immune system won't typically attack it because it wants to avoid attacking its own liver. So the pathogen is safe. This is called molecular mimicry. But the mimicry isn't perfect, so sometimes the immune system does become sensitized to the pathogen, attacks it, clears it, and starts slowly attacking the liver (or whichever tissue bears the same epitope as the mimic). It shows up years later as an autoimmune disease, but the data just isn't there to isolate its cause to that pathogen.

So the best strategy, if we can pull it off, is to vaccinate against the original pathogen (or prevent it via other means... clean food and water, etc), but to target epitopes which do not resemble any human tissues, and with adjuvants that do not sensitize the immune system against any human tissues.

As for how long adjuvants stay in the body, it's definitely worth studying more, but their whole function is to sound the alarm, so I'd expect that they're cleared rather quickly. Anything that fails to do that is by definition not an adjuvant. But assuming that an inappropriate response was triggered in the first place, you'd see the same effects whether or not the adjuvant was still around: If the initial exposure has triggered clonal replication of whichever B and T cells attack the antigen, self or otherwise, they'll stick around in your lymph nodes for years and years, and they'll re-up their numbers with each subsequent exposure.