Not to take anything away from the tuner but, exhaust can make a world of differance.
Here is a great example, this is going from 1 3/4 headers to 1 7/8s and a new Y. Look at the TQ it picked up in the mid range.
http://www.ls1tech.com/forums/attachments/dynamometer-results-comparisons/253996d1284674798-speed-inc-tuned-h-c-i-a4-346-495rwhp-426rwtq-arh-ewp-flowmaster-dyno.jpg