Right - I've spent most of this evening faffing round with the xbox and I believe I've made a much better connection with the PLL_BYPASS.
The point that was causing me trouble was the POST_OUT1. I removed this thinking I would improve the joint as there was little solder and I thought a quick jig with the wires wouldn't hurt.
Now, I couldn't get the damn thing on and when trying to remove the glue (further down the wire) I actually pulled the wire clean off, pulling a lot of the solder with it (DOH!).
There was only the tiniest bit of solder left, smaller than the point of a pin. I tried to add more solder but it wasn't happening and I was concerned about damaging the pad. So what i did was tin the wire with excess solder, line the wire up and apply the soldering iron on top and fixed it in place. The connection isn't as smooth as I would like it and I don't really think it's a great joint at all, but the console boots up just fine (I think the solder is joined to the board more than anything).
What i'd like to know really, is if the console is put at any risk from this solder joint not being too great? i.e. spontaneous combustion (obviously worst case). It's at this point that i'm really kicking myself for not taking any pictures before putting the thing back together.
I'll also update tomorrow when I get home from work, with if I've resolved the cold boot issue.