I've been having a lot of medical appointments lately, and I am asked this nearly every time. (And then my BrE-speaking friends ask me the same thing when I say I've been to the doctor's.) It has struck me as something I'm not accustomed to being asked (and not because I'm a stranger to doctors!). So, I've had a look on the internet, and found that how you feel in yourself is used on American sites, but it tends to be referring to something more like self-esteem than how one feels physically, as in the following examples:
When you act as if you are confident you will not only feel it you will appear it to the world around you and you are likely to find this magnifies how you feel in yourself. [sleepingtiger.org]Now, at the doctor's office, I'm definitely being asked about my physical self, not my psychological self. But I don't recall being asked this when under the care of American doctors. So, the question is: is this an AmE/BrE difference? Let's ask you! If someone asks how you feel 'in yourself', how would you interpret it? Is this something you're used to hearing in a medical context?
There is a tie---an invisible umbilical cord---between how you feel in your body and how you feel in yourself. [firstourselves.com]
Postscript (18 Nov): Just saw an ad(vert) for Danone Activia pro-biotic yog(h)urt , in which the woman who took the "Activia challenge" says "I feel healthier in myself" (thanks to the yog(h)urt, apparently). Checking out their UK website, it says: "It helps keep your digestive system ticking away nicely in the background so you can get on with life more easily and feel more comfortable in yourself." There are videos of their ad(vert)s on the 'Testimonials' part of the site, but they're not downloading for me at the moment--but they might allow you to hear the use of in myself by a native speaker. In the US, the company is called Dannon and they market the same yog(h)urt, but there's no in my/yourself on the US website.