How many diseases can be linked to disruption in the microbiome of a human?
It is an open question and an active area of research. You will not be able to get a definitive answer to your question of number, as each new discovery will add to the total.

As for repopulating, we have not even determined all of the strains of microbes that populate us, many are very difficult to culture in vitro, and we do not know of all the functions for each species, so we do not have a clear picture of which need to be there, which don't, and whether or not some species work together to provide us with a benefit. For certain conditions such as Irritable Bowel Syndrome, one of the treatments that has been tried is fecal transplant.

Do a literature search for recent reviews. Nature Reviews tend to do detailed reviews, especially on topics as in the news as the Human Microbiome. That is probably the best first place to start. Then you can start to drill down into the reference papers that are cited in the review. That will generally give you a good state of play in the field.