This is a pretty broad question, but I will try to give an answer:
This process will undergo further evolution over time, no question. It has evolved into the current state and there is no reason to assume that this ended. When there are mutations which prove advantageous, they will evolve. This may also involve a faster response time for example, but we can of course make not definite claims about it.
There are antigens which are not recognized by the immune system, the process is called molecular mimicry. In it, microorganisms mimic molecules or structures which are found inside the body of the infected person and which are therefore not recognized by the immune system (if the immune system recognized self-antigens, this leads to autoimmune diseases). Have a look at the references 1 and 2 for more details.
This is a rather theoretical question. Our immune system is really efficient in clearing potential threats before you get a real infection. You can see the difference when you compare healthy individuals with persons which are immuno suppressed because of a transplantation. These persons need to be very careful about their environment in avoiding the exposure to potential pathogens. And they easily get infections. Additionally microbes evolve to evade our immune system. So I think the answer here is no.
These are viruses which co-evolved with the organism, an example would be the ebola virus in certain fruit bats. Here it does no harm, while it is a big problem for humans. As there is a really, really big number of viruses available in nature, it is quite unlikely that we learn to tolerate all of them. Additionally viruses mutate and change over time, so we would have to learn again to live with them.
- Molecular mimicry
- Molecular mimicry and immune-mediated diseases.