More importantly, you have an E350 van with a 5-speed manual trans????????? COOL!!
I don't buy the hype of cryogenic rotors. They are probably quality units, but I'm not sure the cryo does much at all. It's all about getting the heat out of the rotors before you stop and sit, and making sure they're true when you mount them up. The pulsing you feel is not because the rotors are warped, it's because they have thick and thin areas. This can be caused as a result of rotors being warped, but it also can happen because they had some runout when they were first mounted. It's called DTV, "diametrical thickness variation".
You can spend big money for rotors, but no matter how much you spend, mount the rotors up w/o the tire and wheel and use a dial indicator to make sure they don't have any runout as they're turned. More than .003" of runout will quickly lead to DTV and a pulsing pedal. Put lug nuts on to hold the rotor, put the dial indicator against the side of the rotor, where the pads contact it, and watch the dial as you turn the rotor. Any more than about .003" and you're going to get pedal pulsing again. I've seen new rotors with as much as .010" of runout that is the rotor, not the hub. Even though the rotor is new, it's junk.
FYI, the slots help to keep the pads in contact with the rotor when the brakes are HOT and the pads are off gassing, the holes add more cooling surface to get the heat out faster. People who buy into the cryogenic treatment are looking for MAX performance, so that's why you're seeing the three together.
Honestly, if you check runout on the rotors when you mount them, and make sure the rear brakes are working well, along with trailer brakes, you'll be fine.
The van you have was likely a) Abused, b) Neglected, and c) Serviced by someone who didn't give a crap.
Good luck!
Chris