Increased Idle During Decelleration

Howdy Y'all,
I've been reading tutorials trying to find the best way to get started on tuning the L59 LS engine in my 2004 Chevrolet Tahoe. My immediate goals with tuning are to find a good balance between improved power and mpg. Here are the mods I've done:

*) Doug Thorley 4-2-1 long-tube headers
*) True-dual exhaust with X-pipe and used mustang mufflers
*) Swapped in a T-56 6-speed manual transmission in place of the stock automatic transmission
*) Swapped 16" factory wheel tire combo to larger 18" rims and smaller diameter tires
*) Made slight incremental corrections to the VE table based on log data

The VE table changes I've made were related to data logged while driving. I've read that this is the first step in tuning for most LS engines...the second step I have planned is MAF tuning and once that's completed I'll be doing fuel and spark changes.

After the T-56 swap I fixed all check engine errors due to the automatic transmission being gone. Then I configured the speedometer due to the wheel/tire change and T-56 swap. I also wired the automatic shifter switch to stay in "2nd" so that the truck starts. All features such as ABS, speedometer, and cruise are working fine after my initial tuning changes related to the transmission swap. When decelerating, either while coasting or braking, I tend to either push in the clutch or shift the transmission out of gear so it's in neutral. As the truck is decelerating once it gets to about 35mph the engine idle comes up from it's normal level (500-600RPM) to anywhere between 700RPM to 1200RPM and stays there until the speed has dropped to 10mph.

My question for you all is how do I identify and correct what's causing the idle to increase? I have a recent tune that this behavior is easy to repeat that I can upload. I can also log data while this occurs, but I will need some suggestions on *what* to log - I expect that I'll need to log at least speed, air/fuel, throttle position, and manifold pressure, but I'm not sure what else I'd need to log.