If you are using a LS2 block the knock sensors and the cam sensor are different for starters. You can buy a conversion harness from Casper Electronics
http://www.casperselectronics.com/
The IFR rate should be correctly changed. I would not add 40 %. Use one of the Excel spreadsheets to figure it out. Its a constant value that should not be touched after it is recalculated.
I have had very good luck in getting the 90mm TB's to work by changing B4349 to .0157 to tell the PCM the effective throttle area has changed.
Set the coolant fans as well and you should be OK to get it moving!
Howard