--Magnet-responder
LimeWire has no influence on it.
LaunchServices picks the first application in alphabetical order which can handle the appropriate protocol.
Your only option is to rename Acquisiton to xAcquisiton (that's what stief does).
--inserting magnets
Hmm, LimeWire can detect magnets in the clipboard but the code is only enabled on Linux machines. Post a request to enable it on OSX as well.