Nothing wrong with cutting coils, just go easy and you'll be fine. I've done it on a few first gens, all with great sucess. I haven't done it to a 2nd gen yet. The coils are shorter. When cutting coils, you just don't want to cut too much off. That's when it'll drop too low and the ride will suffer. Most coils are flat on top, so when you chop it, it's no longer flat. This isn't really a problem, but ideally it's best when a coil is flat because it won't want to bow like one that isn't flat. I cut the very top flat so it won't wear through the rubber pad and squeak.
You can always buy some Sittin Sic coils, but they're only about a 1-1/2" drop. If you want 3" of drop, definitely go with a set of DJM arms and don't try to get 3" from a cut coil. I'd never cut more than about 1-1/2" rings from a coil, any more is just too much from the coil itself, and is when it's time to think about some arms instead.
The truck in the first thread below had 1-1/2 rings removed, the 2nd thread 1-1/4 removed, both trucks had the b/j flip. A little different than your 06. My advice to you is get some DJM arms to get the 3" you want from your 06..