re: If people start having serious long term side effects from the vaccine

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Science cannot yet explain the causes of autoimmune

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This isn't exactly true. We know quite a lot about it. Every human has autoreactive lymphocytes. We know there are two ways AI disease can develop, through failure to develop tolerance to self-antigens, and dysregulation of some part of the immune system that leads to loss of tolerance. We know that infectious agents can cause aberrant activation of tissue antigen-presenting cells which cause T-cell auto-reactivity, and there are several features of pathogen evasion, from molecular mimicry to superantigen activation, that provoke auto-reactive responses. We also know what genes are linked to autoimmune disease, and what HLA alleles are linked to autoimmune disease. We can even test for autoantibodies that are fairly specific for certain diseases. Suggesting that the adverse effects of vaccines will modulate an autoimmune route, as though it couldn't possibly modulate disease pathophysiology, is frankly a little weird.

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t has been proven that there is a link between the 2009 Pandemrix vaccine and Narcolepsy, but they can't exactly identify why.

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This link says otherwise? LINK

I will read your link later, but the writing style of the author is pretty annoying. I don't think they are a scientist writing for other scientists, looking at their publication record.

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So how can you be so certain that something similar could not possibly be happening with covid vaccines?

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Firstly, I'm just extremely skeptical that the long-term effects of the vaccine would be distinctly different from the long-term effects of natural infection. Secondly, the association with vaccines and long-term disease rarely ever plays out, and this has happened time and again, with every new vaccine. People don't remember the panic with the diphtheria, tetanus and pertussis vaccine in the 80s, but the accusations were similar. And vaccines with high injury rates tended to produce injury fairly quickly following injection. The notion that they will absolutely produce long-term effects at rates higher than they would exist in controls, as a surety, is something that has been offered as a caveat for vaccines before, and it really hasn't been proven to be the case.