I’d change the pick list of Aliens to being a list of creatures/army types from 40K and I’d have each planet being a host/legion/army of the enemy. The Orks or Eldar aren’t going to be wiped out on one planet. I might even just make the enemies be predominantly from one race for 5 or 6 missions (remembering that something “outside the box” should pop up every 4 missions or so… Inquisitors, Ordo Malleus, a mysterious psyker that must be captured alive and so on).
I’d also be tempted to give the enemies something like two Special Abilities per session. F’rex, Tyranids and Genestealers using Isolate and Ambush, or Ambush and Lasting Wounds, or Lasting Wounds and Exploding Bodies.
Leaping would do for Swooping Hawks or Jet-packed Orks, it’s a nasty ability when used to keep some PCs in combat while booting others out.
Corruption? Every time you use a Weakness that’s a Corruption. When you hit your final Weakness then it’s “Betrayal of the Emperor”.
Guns map pretty well to 40K equivalents and won’t need much changing… Lascannons, Autocannons, Heavy Stubbers, Bolt Guns, Shuriken Catapults, Lasguns, Flamers and so on are easily matched up to their 3:16 versions. If someone improved their Flame-Gun a lot then make it a Heavy Flamer, etc.
I’d add a finger to 3:16′s 4-fingered PowerClaw… and make it a PowerGlove or LightningClaws. 
Different levels of enemy are really just described in the fiction. Have “Bosses” cause kills if you roll well, while lesser enemies fail to attack on poorer rolls.
Grenades… I’d keep them the same Kill-wise but in the fiction I’d want to know if they were Crack, Frag, Melta, Virus, Toxin, Vortex and so on. Maybe smoke would give you the ability of Reduce Visibility on a successful NFA check? But I’d want to know the fictional colour of Marine or Guardsman Volkhammer’s grenades when he’s throwing them.
And 40K has such awesome colour and background. I’d want to know when people flashback what shit-hole they were born on and what they did to end up in the Marines, Guard or Arbites. You can really go to town in Flashback on who the characters are and what traits define them.
I’d make it almost mandatory that a Weakness displays some heretical action or mental deficiency that allows for corruption or complicity with Horus, the Warp and the Emperor’s enemies.