I have done a 2008 regular cab short box silverado exactly like you are talking. You will need the main engine harness since the 6l90 uses an internal tranny controller. You will also need to deal with the reduculous huge output shaft yoke on the 6l90e, it shocks everyone once they see what they have to deal with on thsat yoke. It all fits just fine though on a stock floor height, no body lift was used and it was for sure the taller 6l90, not a 6l80e.
I do see one problem you will have though, the years have to be matched between the tcm inside the trans and the year of the main engine pcm. 2007 to 2009 use one tcm to pair up with the 2007 to 2009 pcm, then in 2010 and up, you need a 2010 and up tcm. Another option could be to use the newer pcm in your truck, but I am not sure if that is possible.
You don't need the 6 speed cluster and shifter, it works just fine with the 4 speed stuff, you just can't select shift gears which is useless in performance driving anyways. A proper tranny tune, just throw it in drive, and let the vehicle shift.
When everything is hooked up properly there is no need for a segment swap. Since the pcm and tcm are independent of each other, they both read as their own modules. Once it's hooked up and you pull the tunes, it automatically shows as a 6l90 equipped vehicle, and your engine stuff is the exact same as when it was a 4 speed.