My CVO FLHTCUSE6 is still stock (I've only had it a week! Give me some time!), but I can relate my experience with Power Commander and Race Tuner on my '05 Wide Glide.
When I had 7k miles on it, I took it from 88 to 95. BIG, BIG heads from Nallen Heads in CO. 10.5 cr, roller rockers, chain drive S&S 585 cams, etc. When I first built it, I installed a Power Commander and had it dyno tuned; 102hp & 103tq. It ran great! I had an intermittent problem with the Power Commander, which they made good by sending another one ASAP. Later, after talking to a very experienced dyno tuner, I decided to switch to the Race Tuner. More dyno tuning; 107hp & 107tq! It's not just the peak numbers either; with the Race Tuner, the torque numbers were much higher from 3k rpm to redline than the Power Commander was from 3k rpm to redline.
Outside of the engine, I have V&H Bigshots w/V&H baffles swapped out for Big City Thunder Monster baffles, and a Ness Big Sucker air cleaner.
Now I have 47k miles on it, and it still runs as strong as ever! Mid 11's in the 1/4 mile.
Just my .02 worth.
Joe
PS this was all done in 2006.