How can I disable the Secondary Air Pump
 

I just swapped motors in my 2000 S4 Tiptronic. My problem just became evident. The replacement motor came from a manual trans S4 and there is no SAI pump used on that model. Only fix is to swap the automatic engine heads from the original motor. That can't be done as they were damaged when the timing belt slipped in a slow speed crash that broke the timing belt cover. Why the manual S4 doesn't use one and the auto does is a mystery to me. I keep reading that it can be coded out but I cannot find out how. I do not advocate bypassing this pump, as a matter of fact a few months ago I rebuilt it by replacing the bearings. Cost less than $5.00 and took about 90 min. But I need to get this car running and cannot afford replacing the heads. Anyone have any insight as to how to disable this warmup method?

You have to alter the code in the ECU disable SAI. It isn't as simple as a vag-com mod. I sent you my email address in response to your PM, I can walk you through it (but be forewarned, it isn't possible with a lot of aftermarket tunes, and requires a substantial amount of understanding).

I would like to know how to do the same. It's a pain in the azz.