The divergence is measured in base pairs not events. That is obvious.
First, it doesn't mean anything if you measure by a different method. You get a different number, but the organisms are still exactly as related to each other as they are by the different number calculated by a different method. Hence, I don't know what your point is here. It's as in my previous post: a distance is a distance whether it is measured in miles or kilometres.
That Creationists are so keen to measure genetic similarities by methods that produce low numbers is curious. Could you explain why you wish to do so?
No, the indels represent 90 million base pairs, the only way you get 98% is if you ignore the indels.
Which, from a check of the scientific literature (though not a huge one) appears to be the standard way of measuring genetic similarity. Not just for humans and chimps. I don't know the reasoning behind this, but most likely have a greater inclination to presume that 'science' will have a good reason to do this than you do.
What is your reasoning for preferring to count the indels, when it appears that 'science' doesn't?
We have no clue what their genomic make up might have been but the fossil record makes it clear, they were much closer to chimpanzees right up until 2 mya.
Given that we know the similarities and differences of the two genomes, we have far more than just a 'clue' about the genomic makeup of the common ancestor.
Except a deletion like that never happens, even gradually over time.
Mitochondrial DNA is tiny, about 16,000 base pairs. Various pathogens and symbionts also have tiny genomes of well under one million base pairs. Given the reasonable assumption (and scientific consensus) that these evolved from free-living organisms (remember common descent of all life), clearly very many base pairs have been lost. Not necessarily all at once (as I described in my post.)
Those mutations are not cumulative, the genome is constantly repairing itself. With billions of humans on the planet we have never speciated and with the cumulative mutations we diverge by less then 1%.
DNA repair is only 99% accurate. That appears to be a high number, but genetic change due to mutation takes this into account. And with a lot of time, the remaining 1% adds up. Please read the descriptions of how molecular clocks are interpreted.
As for the speciation, that depends on what you mean by 'we'. Humanity, in terms of genus Homo, has speciated. The evolutionary tree for genus Homo already has a number of species and more are being found. E.g. Homo floresiensis.
If you mean Homo sapiens, then no, we haven't speciated in terms of a completed process. However, before modern transport increased the mixing of people from different locations, there were small modifications to local populations in order to better fit local conditions. Skin colour, ability to thrive in low oxygen high altitude environments, etc. This hasn't reached the level of subspecies even, but then there is no expectation that any living species should have speciated unless conditions are suitable (different populations with different survival pressures) and sufficient time has passed. There are claims that there were extinct subspecies of Homo sapiens, such as Homo sapiens rhodesiensis or Homo sapiens idaltu, but these are of arguable status and I personally consider the science far from settled.