OP - you have a pretty good list.
The 2.9 upper with the 6# lower is basically the same as adding an 8# lower to a regular Harley blower and a lot of Lightning owners have used that combo for years without belt slipping problems with the right length belt.
SCT 2600 is basically the same thing as the old BA2400 (no longer offered by SCT) so you're good there.
Definitely nothing wrong with the VB
to decrease clutch slippage in the trans during shifts and always a plus to add more capacity with the 4X4 pan.
ported case (Joker) will add more boost and lower downstream temps vs the stocker.
As previously stated - GET A WIDEBAND and FUEL PRESSURE GAUGE !!!!! Your tuner will need datalogs from the wideband to properly tune the truck unless you go to an actual tuner shop that has the A/F probes and dyno.
If you're still running the stock fuel pumps, you'll need to consider going to bigger pumps and a metal 'Y' in the tank and getting close with these mods to needing bigger injectors (60#).
SBTB = good.
With these mods, you'll have a great running truck, but close to the limits of the stock block - start saving $$$ for a new one down the road.