Well , thats the bitch about 360s , you can never know if what you just did RRoD the 360 , or it RRoD by itself, coincidently exactly the same moment you modified things.
I would first remove the board from the metal case, have it completely bare, and look underneath. The through holes where the connections are could have leaked solder underneath , and thats where the bridge is.
Look for any solder splashes that might have occured, cleaning them as needed.
Where was the board when you attempted this? I'm an electronics technician for 10 years now, and yet i still sometimes work in a real mess, increasing my chances of making mistakes. I ripped off a surface mount capacitor from one of the edges of the card, and it RRoD. The damage was barely noticeable. I have absolutely no recollection of breaking that capacitor , yet, it was. Replacing it with one from another 360 located exactly same place (so i didn't have to bother reading the value) fixed the RRoD.
There is also , the possibility where just by moving the board around while grabbing the heatsinks , damaged what was an already poor connection, and what was suppose to happen , happened (RRoD). Although RRoD stay on for more then 2 seconds.
So , all i can see is 1) short 2) damaged part/ trace? (your xclamp attempt , although you tried after RRoD..) 3) Normal RRoD , but you said it doesn't stay on for more then 2 seconds, so again..
Maybe that splash/short is somewhere that isn't powered until the console boots, so that's why you can plug your hd and light comes on , but when the whole circuit boots, it frags due to that short..
Good Luck