If I remember right, it tells you to adjust the primary to .60 +/- .02. Then the next step is to cycle the secondary and it should come out around .72. Let me look for the thread on tps adjustment with tuneecu.

edit: Here it is:

Make sure you read down at the bottom where I finally get it right.

Did not see anything about the secondary throttle positiion sensor jjust idle stepper control valve. Iscv is below the throttle bodies m ptps is on the 3rd throttle body annd the secondary is on nuber one throttle body. I'm getting a code that reads po638 if I rememer right. 2nd throttle curcuit malfunction. That the wording it gives me.
 
well today i fiddled with 2nd tps , removed secondarie plates. put in a new tune. tie wraped the 2ndtps wire to the frame and rode about fifty miles, runs like a mother and no check engine light came on , hope its sorted out,,,, would have rode all day but i had to work. keeping my fingers crossed,
 
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