I failed to read the entire thread before posting my reply, but I put some good info in here, so I will leave it...Sorry!
I would highly recommend the 4L80E over the 4L60E simply based on the weight of the vehicle and the physical limitations of the 4L60E. The cost to properly build a 60 is upwards of $4k including converter and it's limited to ~600hp. The 80 can be built to 600hp limits with less than $2k in upgrades. The cool thing about the Silvy SS/Escalade PCM is that you can segment swap in the 4L80E controls when you have the VATS disabled and you will be good to go! Trans crossmember/mounting will be custom, but that is it!
As for hood clearance, I cannot attest to that, but my recommendation would be to find a cheap stock LS2 car throttle body and intake manifold and swap that on. They look far better aesthetically than the truck manifolds and have better top end. The Vette/GTO intake manifold is a direct bolt-on to the LQ9's 317 casting heads. The injectors and rails will all need to come from the car intake for sure.
The Fan controls are simple as long as the Silvy SS/Escalade PCM is 2005 or 2006. If it is 2003-2004 it will not have the controls as those trucks had clutch driven fans.
You best bet would be to have the harness modified by someone to match your project so the necessary wiring can be removed or added or shortened or lengthened to work flawlessly in your install...
The best option for an oil pan will likely be the stock C6 LS2/LS3 Corvette wet sump oil pan, as long as it clears your engine cradle. http://www.crateenginedepot.com/C6-Vette-Rear-Sump-Oil-Pan-Kit-SSPK-P10994.aspx