Very helpful tool! In stock form, can't handle completely arbitrary fit functions; EQ2ML doesn't convert parameters in expressions such as 'myfitfun(K,x)' to the required m(i) format for fminsearch, since it treats 'K,x' as a single token. This is quickly fixed by adding ',' to the list of delimiters used by FINDWORD, after which it handles that input just fine.
Along those lines, it would be nice if you could specify the fit function using a handle; restricting the 'x' variable to be either the first or last free variable in the handle/anonymous function should allow that.