I have a large backplane board that's full of metal spikes that acted as guides for lining up boards plugged into the backplane. Removing them will definitely break some plastic on the board but doesn't seem like it will affect the actual metal connectors. Should I leave them be or remove them?

They’re fine. Leave them be.

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i remove stuff like that because the extra weight is not worth the lost space in a box when you stack them up. an ounce or 2, even at $5 per is far less than 2 or 3 more 1lb boards at same price. if you are doing gaylords it probably wouldnt matter as much.