1. games made recently ie. (etm, x2 wolverines revenge, hulk etc.) have a SECOND media check, as opposed to the older style games (halo, amped, bloodrayne etc.) which only has one media check. x2 4977 bypasses this second media check, thats why you need it to run newer games.
2. enter the matrix needs patching because the file names are longer then 42 characters, so it patches the xbe and changes filenames to shorter to fit on the xbox hdd.
3. i use boXplorer, i doubt anyone would create a patching type software to run on xbox alone, but it may be possible.
4. i have no clue, buy a new motherboard? (i'm sure a more advanced x-freak will have a better answer)
how did you fry it?