There are a lot of interesting topics in the opening post.
First, the question of interbreeding. As of right now, we don’t even know if there would have been fertility problems between us and our ancestors from 200,000 years ago. Apparently, we were even able to breed with neanderthals to a limited extent, and our populations had remained separate for hundreds of thousands of years prior to that point, so perhaps there wouldn’t have been a problem. The horse and donkey lineages split about 2 million years ago and they are no longer able to produce fertile offspring due in part to a chromosomal fusion that happened in the horse lineage. I don’t think there is any hard and fast rule on the timing of the loss of fertility, but I would say that it is probably inevitable at some point. I would also say that natural selection may not play a role in the loss of fertility. Neutral drift could also fix alleles that prove troublesome for fertility.
The other question is if the human population is still affected by natural selection, and that answer is definitely yes. @glipsnort may be able to cite papers dealing with signals of positive selection in the human genome. The one example that I find compelling is the selection of hemoglobin alleles due to endemic malaria. The most infamous allele is the sickle cell trait which confers malaria resistance, but if you carry two copies it causes negative effects. Therefore, there are both positive and negative selection pressures on these alleles, and that is exactly what we see when we map the prevalence of the sickle trait and compare it to a map of regions with endemic malaria:
There is also a rare allele, HbC, found in population pockets that confers resistance to malaria, and some studies have suggested that the HbC allele may replace the more common HbS (sickle cell) allele in future generations:
“Overall, it generally appears that allele C will quickly replace the S allele in malarial environments. Explicit population genetic predictions suggest that this replacement may occur within the next 50 generations in Burkina Faso.”