is the solder there supposed to connect the two transistors? i'm a complete n00b to soldering and all that, so it seems a bit weird to me.
Magic 3.1 Diagram for V4 (http://www.chipzone.com/installation/playstation2/magic3/V4nogap/v4nogap.jpg)

I see what you mean. The arrow points between them; they look like a resistor and capacitor. I think i remember this point on my V5; i also have Magic 3.1. I believe there is a trace connecting the two components. Look closely and see if you can see a trace connecting the res and cap. If there is a trace connecting them, then it doesn't matter which one you solder to - just make sure it's the correct side of the res or cap.