What are your methods? How often do you test it?
I trimmed my first mobo fine with no problems, but I took my time and tested often. You should test your board after you do anything to it. That way, you know when you made a mistake. Just follow the guides, and rewire everything before you cut it. After rewiring anything, even if it's just a couple wires, test it to make sure it works. When it comes time to cut it, only cut one side at a time, and test between cuts. That way, when it stops working you know where the problem is. I'm new to Gamecube, but it is similar to the N64, just a little more complicated. With Ashen's guides, he practically does all the work for you.
Also, make sure each cut is sanded well. the GC is 4 layers, it is very easy to short between layers when cutting. I'm not going to say what the best tools are for cutting since I've only cut 1 GC, but I use the same method as I did with N64. I use a band saw with a metal cutting blade and cut to about 2-3mm of where I want to trim, and finish it off with a belt sander. If you don't have these, I'll bet a dremel and sandpaper work fine. Don't just take my world on it though, someone like Ashen knows a lot more about cutting GCs.