from what I have read, there are a lot of guys with stock ecms and sct tuners running heavily modified 5.9 mag engines. you can find a lot of good info at dakotart.com. hope this helps.
The SCT Tuner works great. It is what I am using with great ease and success, but the key to them working great is having an experienced tuner map out and load the tunes for you. Sean at Hemifever provides great customer service and excellent tunes.