I'm sure you could find a way to lift the shells of you 3 pending locos if that happens. Or you could just run them without the shells seated properly.
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I'm just dumbfounded that you would be disappointed if they fixed them to be more accurate. I understand that you want them to match, but they do sit at the wrong height.
Either way, IM seems to prefer their locos sit too high
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, so I doubt this will a problem for you.