Yes, that’s correct indels are rare (SNPs make up the vast majority of mutations) but when indels happen they usually affect a string base pairs at once (ranging from 5bp - 1000s of bp) as opposed to 1 or 2. I don’t know whether the 100 new mutations each generation include indels or not.
In addition, several mutations at one site could not be measured if it included significant deletions
Like I said, indels are rare but that counts insertions and deletions. How many mutations do you think are lost due to deletions? And what makes you think this would be a significant number?
It’s worth pointing out as well that deletions don’t affect the overall similarity between 2 sequences. Imagine two sequences that are 200bp long and there are a couple of mutations distributed randomly among them making them 98% similar. (i.e. they differ in 4 positions). Now randomly chop out 50 bases from one of the sequences. On average, that part you threw away will contain 1 SNP and 49 identical bases. Of the remaining 150 bases that can still be aligned, they will still be 98% similar since there will now be 3 SNPs over 150 bases.
You haven’t established what exactly is suspect or why it is suspect. In any case, tens of thousands of geneticists disagree. Just out of curiosity, how do you explain the fact that you seem to stand alone against the tens of thousands of geneticists who think the methodology they use is just fine? Do you think there is a vast conspiracy underfoot?
This is true to an extent. Mutation rates in a given sequence do differ between distantly related species. But we were talking about humans and chimps and humans and chimps both have very similar mutation rates so it seems most reasonable to assume that our common ancestor would also have had a similar mutation rate.