Unicode.
Symbol only allows space plus 223 other glyphs. You need to get several thousand characters in. So Symbol is not suitable. Also, as “This font will not be used by humans, just by another software program in development, …” there is no reason to use a Symbol font as far as I am aware, even if you had only 223 glyphs or less.
The plane zero Private Use Area, which runs from U+E000 to U+F8FF hexadecimal. It is probably best to start at the low end. I would suggest starting at U+E001 for the first glyph, then using U+E002 for the second glyph and so on. I cannot justify not suggesting starting at U+E000: it is just that there may possibly be historical legacy issues over using U+E000 on some Windows platforms. I could not say that there would be problems, it is just that I would avoid U+E000 myself, just in case.
I use the Unicode Private Use Area a lot. The following thread might perhaps be of interest.
I hope that this helps.
William Overington
21 March 2009