Do you further agree that it follows from this that there is some hard limit to which it makes sense to self-modify to avoid certain negative emotions?

I don't agree that it follows, no, though I do agree that there's probably some threshold above which losing the ability to experience the emotions we currently experience leaves us worse off.

I also don't agree that eliminating an emotion while adding a new process that preserves certain effects of that emotion which I value is equivalent (morally or otherwise) to preserving the emotion. More generally, I don't agree with your whole enterprise of equating emotions with utility shifts. They are different things.