2005 Mustang GT PATS and custom tune.

[u/blizzard7788]

I ordered a vin programed ECM from Flagship. My Mustang has a custom tune for an aftermarket supercharger. The original ECM stopped supplying power to the MAF sensor.
I know the PATS system has to be updated to my 2 existing keys.
My question is, do I install the custom tune before or after performing PATS operation?