The TPS alters the ignition timing by a fair margin. You will need the TPS plugged in even if not attached to the carbs.

Two ways of going about setting it up. Take a voltage reading from the TPS with the throttle fully open then set the TPS to this reading once removed. Or remove the TPS and run the bike altering the TPS position until best power is found (this is not fully advanced!).
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If I have to take the carbs off once more...