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as you can see near the empty holes some marks
The marks shouldn't be a problem. If your solder iron tip slides over a pcb trace, it can cut that trace. (Which is probably what happend with the trace going to hole one (the square one top row left side))
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the iron was slipping sometimes too
Which is because you have to add a lot of pressure on it, due to it's power being to low or it's tip being oxidated so that the heat transfer is bad. Also make sure you use the correct solder for electronic work. The solder should melt as soon as you touch it with the tip of your solder iron. The moment you need to add pressure, there is something not right. Sometimes, on very old pcb's, the solderings can be oxidated, so you need to add a little pressure. Usually, adding a bit of fresh solder to that soldering solves this.
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After I installed the thing (Forgot the name black thing with pins that joins the mod chip to the board,
That thing is called a pin header. Trying to desolder it again will very likely make things worse. It's 10 times harder to desolder one than to solder one in.
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I tried de-solder wick which wasnt doing the job, I was having trouble just getting the old solder to melt
I already explained the possible causes of that. The cupper wires in desolder wick can oxidate as well. I always cut off the first piece of it. If I have used it to remove some solder, I cut the first piece which already contains some solder so that I have some fresh new flexible cupper string. Make sure your solder iron is at least 30 - 40W to use desolder wick. A 15W iron won't do the job. Practice a bit on an old pcb of a piece of junk before you experiment with the xbox motherboard. Your local electronic store will probably have some defective clock radios or vcrs that contain pcbs to experiment. If you never soldered before, ask him to show you how soldering should be done, or try to find some instructive video's on youtube.
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the pcb may fix it would it not, as that bypasses the standard connections no?
To rudely say it, in your dreams maybe, but in reallity no. The rework pcb for 1.5 and 1.6 xboxes only connects some points on the mobo to the lpc holes. Those connections are needed for the modchip and were there on the older xbox versions. Microsoft removed them in an attempt to make modchip installs more difficult.
Your frag is probly caused by a pcb trace that got damaged. One that easily gets damaged is the D0 point, as that one isn't really designed to connect wires. Specially the top layer D0 point is a so called "via". It's actually a very small cilinder that is used to connect pcb traces from the top of the pcb to the bottom, and to the layers in between them. If you heat that one to long, it might stick on your solder iron tip. The bottom point D0 is a bit bigger, but I have seen cases where it was totally gone, together with a few inches of the pcb trace running to it. Reconnecting both ends of that trace with a small wire fixed the frag in that case.
regards.