For adventure ideas, I would look into Space Hulk (the board game). There are a few fan sites still kicking around with fan-made missions. These will give a good idea of what a mission might look like, and nearly all of the published missions were a part of a larger campaign. You'll also have maps, which might help make GMing easier. You can also modify the largely Genetealer opponents to other xenos or even Marines or lesser dameons.
As for opponents, that's a tough one. I've only played Deathwatch twice (but very familiar with 40k), so bear with me. A Carnifex is out of the question. While I was a part of a 10 man squad that took a Hive Tyrant, that was mostly the GM's fault (and there being 10 marines firing on it with heavy weapons). A single Broodlord might not be too bad, especially along side a handful of Genestealers to prevent ganging up. A small number of Chaos Marines should be doable, as my rank 3 Librarian recently killed 4 no longer Loyalist Marines with a single Smite (pushed, mind you). Basically, you want to look at the scale. Such an end boss should be a rough fight, but such a fight should only have one "high level" opponent. The rest of the fights should be easier. Maybe small hordes of Genestealers or Chaos Cultists (with respirators/voidsuits, of course).
Two things to keep in mind. 1) Not every encounter needs to end in death. If the squad is overrun by Chaos Marines, they may simply choose to leave, having bested their opponent. Or they could be low on ammo, or in the middle of some other task and not wanting to press the attack. 2) Space Hulks are massive collisions of voidships, so they may very well have several different threats on board. Maybe some Orks took root in another section of the ship, near where the squad is fighting a Genestealer infestation. Or maybe a small Dark Eldar force was looting the hulk when they too ran across some daemons. This will help drive home the size of the ship and the ever present threats to the Imperium. Plus, it'll keep the game from going stale fighting just one opponent.
Hope that helps.