How did you handle star ship combat? As I would consider that pretty shoe-horned. Also computer hacking if you had a cyberpunkish setting.
We did it for our last Epic 3x campaign, no shoe-horning required. (It wasn't 4e, and I don't know 4e, so I can't judge for that ruleset).
We spent lots of time planar traveling via the Astral plane on an open topped ship with sails, that could enclose itself into a force bubble for more corrosive alien atmospheres (traveling to the Far Realms...) If the vessel needed to look like the Enterprise or Firefly, build it that way, but for our setting a sailing vessel worked for our needs. Actually the engine was a artifact that consumed magic items to fuel it, so we went around on Epic adventures saving the multi-verse amassing our treasure while picking up extra magic to feed the ship.
D&D energy weapons: fire, sonic, cold, heat, electrical, positive, negative, whatever was a pulse or focused channel energy attacks. Heavy ballista firing alien heavy materials might cause structural damage. So I might adopt 2e or 3e structural damage rules for a ship's defenses. How about a mental blast (psionic blast intensified perhaps).
We also eventually conquered a created race of adamantine golems, dismantled them and used them to create an adamantine skin onto the hull of our ship granting it DR 10/Scrutctural...
The computer hacker, is a rogue with class skills in Knowledge (coding), Use Cyber Device. He's got Trapsense (detecting countermeasures) and disables devices as required. Perhaps using his Craft skill to jerry-rig bypasses around security hardware, and Profession: hacker...
Remember Pathfinder Advanced Players Guide features the Alchemist new class, and can easily be adapted to a number of steam-punk, cyberpunkish settings as well. Still absorbing the APG to judge best.
Come on give me a challenge that will stump me!
Sci-Fi to D&D is easy peasy.
GP