How much is too much in a 100,000 words book, and when do you think you should really use them? I get the feeling that I have been using them too much, and I recently commanded Microsoft word to search them and hunt them down. However, I find it hard for me to execute them, even when I know that my sentences would hold out fine with a little culling.
I'm not sure there's a set number. The only time it's a problem in my opinion is when the reader notices which would probably happen at a different rate with different people. This would apply to anything you think you say too much, I know I have tons of favorite phrases, sayings, words, etc that I'm always questioning whether or not I'm using it too much. But if you are using it frequently and the reader doesn't consciously notice it and is not thinking "Oh, he used that word twice in the last paragraph..." or something like that than I don't believe it's a problem. The reader in this case could be you, do YOU think you're using it too much? Since you started this thread I have to assume that when you were proofreading you were noticing that those particular words are being used too much, or at least might be used too much, which in my opinion and for my own writing would be enough to make some adjustments. I hope this helps.
It's not a matter of "how many times am I allowed to use it," it's more a matter of how it's being used. Himself and herself are words. They have uses. Sometimes they're necessary to clarify a sentence. Sometimes they're unnecessary. I find that they're most unnecessary when used in what I call "reflexive" writing (because I know no actual term for it), such that himself/herself/myself is being used as an extra, unnecessary layer. Something like this: He felt himself growing warm. Why hadn't he turned off the heater when he had the chance? Things couldn't possibly get any worse, she thought to herself. But of course, she'd likely be proven wrong. They're really just taking up space in these sentences. Padding, more or less. However, in something like the below, I'd argue it's necessary: It was like a dream. I could feel myself walking but I had no notion of moving my legs. It's different in this case because it's different. It's not the default. Obviously, one would normally feel oneself walking when one walks, eliminating the need to point it out. But since this is a departure from the norm, "feel myself" is a good way to add clarity. It filters, yes, but the filtering matters here. Ultimately it's a judgment call, and it's one that comes with time and experience. But just like every other sentence in your work, go through it and make sure all the words contribute. Cut out any freeloaders (and add anything that's blatantly missing).
And an idiomatic sense of where and when to use. You can slip reflexive pronouns of this kind into uncounted places as a sort of optional extra where they are grammatically correct and fine to use in that sense, but add nothing, or when read/heard by someone for whom English is native, they feel unusually out of place. The examples given by @xanadu above are good examples of both where they serve little purpose (the first set of examples) and where they serve in a more logical and needed capacity (the second bit about walking).
To be a bit more specific, and at the risk of repeating what Xanadu already said, I'll use the same examples since they are good ones. In this example we have filtering. The thing, warmth, is being filtered to the reader through the verb of feeling on the part of He. You could as easily say, He grew warm, or you can take Him out of the syntax and say The room grew uncomfortably warm (in keeping with the next sentence in the example). Once we know who's in place (Him), we don't need to be told who is doing the feeling, unless that fact is important, one person feeling something that someone else doesn't or to a different degree, etc. And we need even less to be told that the feeling he is experiencing is his own, rather than someone else's, which is just about the only logical purpose the reflexive would serve there. Another good example. Unless the story contains telepathy - and it could - who else would she be thinking her thoughts to but herself?
