What do I do when a co-author takes too long to give feedback during the peer review process?
It seems you are following your boss' (good) advice. Dealing with co-authors is not always easy as you have experienced. I think I have experienced a similar co-author, not responding but complaining whenever something happens. In my case, the co-author was definitely over-committed and the actions were basically a symptom of frustration about not being able to perform. Now, I think you have done the right thing to a point. The only thing that would have improved things would have been to provide the co-author with the information but with a strict deadline but not more than a week or two. Doing so at all stages, is the only way to deal with such cases. It is not very nice, or comfortable, but it is necessary to make a stand and convey the seriousness. In your case you have clearly had a lot of extra work due to the (lack of) actions from your co-author. I assume he has not apologized?

So what to do? Well, I would write and state that you are sorry the co-author feels left out (or however the co-author has phrased it). You can then state that the lack of response earlier made you assume the co-author was not prioritizing the work and that based on suggestions from your boss you have now taken the actions you have to get the material published. Be brief and courteous but do not add many excuses.