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A lot of the lag on my server is from pipez with ultimate upgrades in them where ultimate upgrades have been used basically everywhere. Would the lag be reduced if these were replaced with lower tier upgrades?

Yes, higher upgrades produce more lag. This is especially the case for item pipes, since the lowest variant doesn't transfer every tick.

thanks, do any upgrades on the item pipe NOT transfer every tick but allow a stack to be transferred at a time? If not would you consider adding "eco mode" to the ultimate upgrade pipes so that they slowly pull out full stacks?

You can fully customize the rates in the config.