I haven't actually read the Boatmurdered saga, so I can't give you any specifics, but turning a DF fort into a DND campaign shouldn't be a problem at all. With Boatmurdered's history already laid out, you've got the story background for the campaign, which simplifies things a lot, as you've got a timeline and major events such as sieges, megabeast attacks and so on, as well as story fluff (families, artifact crafting, births and deaths, nobles ordering people to get battered to death and so on) to make the setting feel more alive. It could also problematize it though, if your player group already knows the story of Boatmurdered, as any major events would be predictable (even though a replay of a historic event probably would end up different due to player choices and dice rolls), which would make the story stale.
First of all though, throw away any idea of transferring DF professions into DND classes. While you on some level can equate an ambusher to a rogue/ranger and a hammerdwarf to a warrior and thus make the conversion simple for those classes, there's a lot far more ambiguous or simply uninteresting ones, such as lyemaker, plant gatherer and cook and so on. What I'd do instead of building the character up around the DF professions, is that I'd premake / let the players make their dwarves, then figure out what DF profession their character likely would fall under based on their class, stats, personality, preferred gamestyle and personal desire - for instance, if you've got a guy who rolls a dwarf rogue with high social skills (CHA) and trap know-how, you could say he fills the job of a mechanic and bartender in the fort. This can (and should) have impact on what happens to that character during the actual roleplaying, but for what's actually put on the player's character sheet, the fact that this dwarf is a mechanic and cook in DF-terms is completely irrelevant.
Basically, let the players build characters as what they like using the standard DND character creation (without wizards etc. if you want to stay true to the DF setting, of course) then see if they'd fit into some DF profession niche which can be used as roleplaying tool by the DM and players throughout the campaign.
Deciding the setting should be the first step for the DM in planning the actual campaign. I'd think I would either run a party of dwarves during a "random" year of Boatmurdered's settled story, or have the party be explorers finding the abandoned for many years after its glory days.
If you'd go for a story during the fort's life, your campaign will be somewhat atypical to standard DND, as it usually revolves around exploration and combat more than social interaction and city dynamics. That being said though, there's always plenty to do in settled situations - detective work (who let those burning puppies out!), general mischief (let's put this goblin corpse in the town well!), subterfuge missions (The baron's a prick - let's kill him and take his place!), cave exploration (okay, there's a candycane down below. Go take a look, lads.) or any other scenario that could take place in a living dwarven fort.
For a post-fort exploration type of campaign, you'd be more back to the basics of DND, with dungeon-crawling and monsters galore. Thanks to DF's detailed storykeeping and the probably existing Boatmurdered maps, most of the work is already done for you - the dungeon layout is mapped, although you should modify it to make the fort more or less linear (depending on what you prefer - linear dungeons are easier to plan out when it comes to events, while nonlinear dungeons means the sequence of events can be shuffled, which the DM can use to vary the outcomes). Think old fort - caveins causing rubble to block passageways, or entire dormitories and storagerooms filled with magma or water, and yet other rooms overtaken by cavern denizens, the offspring of ealier tamed creatures, overgrown, muddied underground jungles and maybe even a clown or two.
I feel either choice would have a ton of possiblities, as long as you keep it creative and fun. I'd advice you against simply doing a rendition of Boatmurdered events played by your player characters, though.