Look at this old post over GMFS, it'll give you a better idea on how to install them to a stock Y pipe:

http://www.gmfullsize.com/forum/show...ghlight=y+pipe

 

you get a pair of 3 bolt flanges to mate to the thorleys, you just cut the stock y right in front of the cats and weld in their flanges and your good, but it only works with 05 an older y pipes. the pic in the above link shows the stock y-pipe for an 06 which is after gm moved the cats up higher in the y, which is why they had to remove the cats to make it work.
05 and older with the cats where they need to be

06 y pipe with the cats moved upstream,doesnt work with thorleys, bassani, or any other midlength

 

You're correct, the '06 y pipe has the cats moved forward as you described but it can be done. Just cut them and weld them back on the stock y pipe. It's easy.

That's how I did it in my '06.

 

you cant go wrong with thorleys. I did the install and was suprised how well it went. My truck is 4wd and had absolutely no clearance issues. As far as a y-pipe goes youll have to get one made. Ill take some pics and post em.
After install and a retune I noticed and increase in power especially at lower rpms and it takes less go pedal to get up to speed.

 

yeah you could do that but there is alot of differences in the y pipe, like bends in the wrong places and such, and if your igoing for stock look to pass a visual you might fail if your y pipe has been butchered up, i know you would with the smog ****'s around here. i got lucky and found a friend to swap me y pipes