I believe 499 would have been written CDXCIX. 994 should be written CMXCIV. You only use a single letter prefix to subtract (hence VIii not IIX) and you only use the two symbols prior to the one you're subtracting from, so you can subtract C or D from M but not X or VI.
This kept complexity of parsing down but also produced fewer forms that could be confused with real words!