Hopefully, all you need to do is add a meta tag to the top of your HTML page that specifies the correct character set (e.g. <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
) and match whatever encoding your datafiles are expecting.
If that doesn't work, ensure that you are using the same character encoding (preferably UTF-8) throughout your application. Your server-side scripts and any files that include text strings you will be adding directly to the response stream should be saved with that single encoding. It's a good idea to have your servers send a "Content-Type" HTTP header of the same encoding if possible (e.g. "text/html; charset=utf-8"). And you should ensure that the mobile safari page that's doing the displaying has the right Content-Type meta tag.
Japanese developers have a nasty habit of storing files in EUC or ISO-2022-JP, both of which often force the browser to use different fonts faces on some browsers and can seriously break your page if the browser is expecting a Roman charset. The good news is that if you're forced to use one of the Japanese encodings, that encoding will typically display right for most English text. It's the extended characters you need to look out for.
Now I may be wrong, but I THOUGHT that loading these files via AJAX was not a problem (I think the browser remaps the character data according to the character set for every text file it loads), but as you start mixing document encodings in a single file (and especially in your document body), bad things can happen. Maybe mobile safari requires the same encoding for both HTML files and AJAX files. I hope not. That would be ugly.