Indeed, I recommend using Microsoft Keyboard Layout Creator, which is a free software and very easy to use. I've used it before to make my own custom keyboard (which I'm using right now, in fact, and I use it all the time as my default keyboard), and it allows me to easily type diacritic marks using deadkeys (àéïôū etc. are a breeze) and other special characters like æ œ ł ij ȷ ® š ð ſ ŋ þ ž × ç ß etc. which are otherwise more difficult to input.
Just last night, I made a font (based on another opensource font) for the International Phonetic Alphabet using FontCreator, and I created a keyboard to go with it. Now, when I switch to that keyboard:
i kan taip ˈjuziŋ foʊˈnɛtik noˈtæʃǝn
It takes a little practice to reprogram your muscle memory to your new layout, but I find it's well worth it.
Method: when you've made your font, print out a glyph sheet containing all the codepoints for each glyph. In MKLC, start from an existing keyboard (easiest), or start from a blank keyboard, and input each glyph using the keyboard or codepoint. NOTE: you can just type <a> (without brackets) to code that letter for a key, and so forth with any other glyph accessible using the installed keyboard. You can also copy and paste glyphs from MainType or the character map. Finally, (what I find easiest for the glyphs not accessible on my keyboard) you can just simply type in the unicode codepoint, BUT you have to ALWAYS use u+ before each code sequence. So, for a superscript n, you have to type u+027f. If you just type 027f or $027f, it will take that as character input rather than code. (But, as a handy side note, you can use this to make a keystroke input multiple characters, even whole words! Sick of typing "etc."? Just program a keystroke, like AltGr+e, to automatically type that string for you! Even better, they still input as distinct characters, rather than a composite glyph.)
Just make sure to warn other people who use your computer, or they'll suddenly be surprised to find the keyboard doesn't work as they expect!