Think you maybe getting confused with the SC pump & the water pump. There is an option to turn the pump on via VCDS and you should hear/feel water passing through the pipework. Sorry I cannot help further as mine is divorced and on a separate loop.
TB upgrade is not essential until you have the charger ported to allow for the extra air flow, spend the money on the remap before going any further. But not APR as they have stop supporting the 3.0tfsi
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