Well, once you've cracked it open, I think you have to go ahead and replace it. You've broken the thermal bond between the heat sink -black metal piece- and the processors. The compound hardens between the two and once pulled apart, you almost have to replace it. First, do you have any Arctic Silver 5 or other quality heat sink compound? Other supplies: 91% isopropyl, wood handled cotton qtips, kimwipes or other lint free cleaning towels.
1) Disconnect the battery connection to proc. board..
2) Using qtips and isopropol, swap gently tops of cpu and gpu.
3) When compound starts to break down (turns mushy instead of hard) use more clean qtips and kimwipes to remove all compound.
4) Do the same with heat sink - black metal piece from top.
5) Be sure to not leave any cotton qtip pieces or kimwipe pieces in between connections.
6) With wood handle piece of qtip, spread an even coating on the tops of the processors and square heat sink spaces (as removed from.) Not too thick. Less than 1/2 thickness of a dime. Do not use cotton end - it'll leave cotton strands in the compound which is very sticky.
7) Line up heat sink to processors, set on top and give a small (<10º) turn so compound will spread over any uneven areas.
8) Replace screws - all except screw that holds "L" pressure bracket on top.
9) Gently bend that "L" bracket down on its ends so you have better contact. This should be done very gently so you don't break it. You don't want a big bend, just a wee little bit to increase pressure.
10) Place bracket on and start screw. Once a turn or two are on the screw, rotate so hole is lined up in bracket and heat sink.
11) Tighten screw. Be sure not to strip it out. Tight but not killa' gorilla tight.
12) Reconnect battery connector.
13) Place bottom on unit but only use a few screws just in case...
14) Turn on computer. Monitor cpu temp. If climbs over 80º easily, turn off, remove bottom and try tightening up screws a bit more. You may have a poor thermal connection meaning compound is not moving heat from proc. to heat sink. Try again. If still climbing in heat, remove heat sink, add a little bit more compound and try again.
Hope this helps a little. Good luck and take your time.