I am not sure, but the shims are used to set gear mesh. By now that machine probably has enough wear from normal use that it won't matter. Keep the oil level where it should be and I doubt you will have any problems. I do find it strange that the shim removal fixed a leak. Perhaps it had been apart before and the previous owner was not as diligent about cleanliness as you are. It probably wouldn't have leaked if you reassembled after cleaning.
Good job. Nice to hear success stories.