I went ahead and just switched from an SPT to a Cobb intake based on Cobb's new recommendations for their new 3.10 maps. When I ran the 3.00 map I did have about -4 to -6 A/F learning with the SPT intake. This is still within the acceptable limits and a tech from Cobb said my map looked fine but said it was the SPT intake that was causing this.
I then switched to the 3.10 map and the A/F went back to 0. So it seems that the new maps from Cobb work just fine with the SPT intake, or at least it did on my car. The new maps are much smoother, make more boost, and the boost comes on earlier. I used Virtual Dyno to plot the runs
I haven't logged a run yet with the new Cobb intake, but I will soon. I'm expecting to see the same power. I picked up the intake used for $80, so it was worth it just to try them back to back to see if the SPT intake really caused a problem.
2005 WRX Cobb Stage 2