Gen 3 vs. Gen 2: Whipple made a revolutionary design change to the rotors. The Gen 3 will make ~ 30 more rwhp over a Gen 2 primarily by efficiency (it takes less power to drive the Gen 3 rotors, so this is basically "free" power)
Gen 4 vs. Gen 3: They made an evolutionary design change to the rotors. All else equal, the Gen 4 will make a little more boost and ~5-6 more horsepower over a Gen 3, per the person I spoke to at Whipple.
The JDM Gen 4 kit with the twin 65mm TB and upgraded heat exchanger is a good setup but I think you are going to need larger injectors than that kit comes with (47 lb/hr).
Also, the Whipple stage 2 kit will make more power with the larger twin 68mm throttle body. It also comes with 60 lb/hr injectors and the upgraded heat exchanger is standard instead of optional...
https://whipplesuperchargers.com/index.php?dispatch=products.view&product_id=331
You can catch this kit for sale at Lethal Performance several times per year at 15% off.
One drawback: JDM's tune is going to be a little more refined than Whipple's. I can recommend a good tuner if you want to have yours dialed in just right, though. You would just need a laptop to run the data logs and some time to go back and forth with him.
I recommend installing headers with the Whipple stage 2 to really let the motor breathe and also to let it roar.
Note: the Whipple stage 2 kit was developed by Whipple for Shelby's Baja 700 trucks back in 2013/2014...
http://www.trucktrend.com/truck-reviews/1506-first-drive-2014-shelby-raptor-baja-700
