Quit disconnecting the battery. It does not accomplish anything more then just pulling the EFI fuse besides also killing the clock and radio memory and powering off the stock alarm's controller (it does not reset the stock alarm). All you're effectively doing is clearing any diagnostic codes which are getting triggered and might actually help you diagnose the problem. The car starting intermittently most likely has nothing to do with the fact that it does start after you've disconnected it a random number of times.... unless one of the battery cables is COMPLETELY shot.
See the MKIII FAQ section for a thread on how to check diagnostic/error codes. Post back with any stored codes after you've run the car a couple times and after a couple failed starts.
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