you're both right, Higer stall speed is like holding the clutch in longer, so instead of engaging a gear at say, 2000 RPM (STOCK GTS sportshift stall), it will raise it to a 2500 or 3000 stall. Even in "M" this would help a bit. 2500 should still be streetable in our cars. it especially helps in the lower gears. With a higer stall, 2nd gear starts would be incredible!
The higer the stall, the longer the converter will go before it "LOCKS"
Shift kits (Valve body calibration) shorten the time between gears (think of a short-throw shifter in a manual car) Not a big deal with the M mode, since you can time your shifts, but it's definitely shift harder and be more responsive (speeding up gear changes
S-AFC2 Won't do much of anything, unless you are just looking for vitual gauges and performance metering, then it's a nice piece, but altering fuel maps and such, it doesn't work.
You'd be best off looking into a powerFC or an aftermarket ECU for fuel tuning. they can also alter Lift engagement, but it does almost nothing in regards to performance (toyota pretty much nailed it from the get go, lowering lift engagement may help a little)