[swaghauler]

The Helo is a major issue as most ports are a "no fly" zone. They could access the ship from the bow by snagging the anchor with ropes and climbing up. An alternative would be meeting the ship in open water, disabled and adrift. This is a very common occurance.
The passage ways in most modern freighters are about 1 meter wide with main passages being about 2 meters; So pistols, sawed off shotguns, and SMGs are in their element here (which is why SEAL's board civilian "small craft," power & sailboats, with pistols). The standard gangway on a civilian sailboat is just 30" wide. A 45 degree list will make it equally easy (difficult?) to walk on walls as floors. At 90 degrees, walls BECOME floors and stairs become "jungle gyms" to climb. If the power is completely out, flooding will be an issue because the bilge pumps are not functioning. You may need to think about putting a time limit on the mission (at which point the ship sinks). The water could "chase" the players from deck to deck.
The fire would be a MAJOR hazard. Respirators would be needed in engineering (if it's not already under water) due to fumes/smoke. Firing any weapon below decks would deafen everyone if not suppressed. 7.62mmN caliber weapons could penetrate the hull (another reason for SMGs). Cargo could be shifting, causing further damage to stairs, doors, and gangways. It would be a regular fun house.