Are the logic board and all the components attached sitting completely inside the computer? My guess is that once you took the bottom cover off, and cleaned it out, some things may have become loose, so when you put the bottom cover onto the MacBook, the aluminium on the bottom touches the logic board and shorts some part of it out. Are there any dents on the housing or on the bottom cover. Sometimes, if the dents are deep enough, the can touch to board and short it out too. These are just a few things to check. You may also want to make sure there aren't any foreign objects that may be stuck in there that get pushed up onto the board whenever you put the bottom cover on.
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