Man, you really sound like you should stay away from electronics, there is so much wrong with what you have written.
The little black things are resistors. Now, if you are lucky they will be just pull-up resistors so losing them will not break the signal, and it may still work, but they are all there for a reason. I'd like to know how you lost a couple anyway, what are you using for a soldering iron?
Simply having header pins on the LPC points wont affect your xbox at all. If you were really messy, there is the small chance that some excess solder might come through the board from the bottom when you soldered it in and MIGHT short against another pin but its extremely unlikely.
Ripping the header out is probably what killed your xbox. You are aware that those WERE plated holes at the LPC points?. That is, the holes carried the signal from one side of the board to the other. The first thing to go when you rip any component out of a hole without melting the solder properly is the plating inside the holes. Its just as if you broke one of the tracks on the board.
You say you saw a *spark* come from your soldering iron?... Jeez man, what are you using?. If you are modding xboxes (and *you* shouldn't) then get yourself some tools. Other people here have said they own several hundred dollar irons, and most of you laugh at them. Trust me, you just don't know. Anyone in any trade tries to get the best tools for the job because it makes the job easier and won't do weird ass things like zap your board.
On this forum there are more and more non-hackers trying to hack their boxes, non-programmers programming and people with no hardware education modding boxes. No wonder the forum is now filled with posts screaming for help.
Your xbox is toast man. Send it to someone with a clue.