Not sure if there's anyone on the board from Amsterdam, so being Dutch I'll have to step in I suppose... However, I don't live there and haven't gone clubbing in Amsterdam for years, so I don't really know about decent indie club nights.
Winston is probably a good call... I think they have a cheap hotel as well, plus it's very central (near Dam square) and pretty much right next to the red light district. So that might be a good place to stay for your stag thing. Dunno if the hotel's any good though... The club itself is pretty small. I've only been there a couple of times in recent years though, and then it was always for gigs, most recently for White Hills.
http://www.winston.nl/
Paradiso probably fits your description too. After gigs they usually have club nights, surely in the weekends. I remember an indie club night called "Noodlanding" from years ago which I think they still do, mostly on Thursdays. The crowd is probably still mostly students, but again, I haven't been there in years. It should be mainstream enough for you though. A big advantage of Paradiso for gigs is that you can usually buy a ticket for one show and then see whatever else's playing in the other rooms as well. If you happen to be there for the weekend of Sunday 25th, you could buy a cheap ticket for Wavves (like 10 euros) and then sneak into the main room to catch Wu-Tang Clan (35-40 euros!) instead/afterwards. That's what I might be doing.
Other "rock venues" I remember from like 10(!) years ago are places like Korsakoff and The Cave, although both are more rock/metal than indie per se. Then there was a pub called Soundgarden, but I don't remember ever seeing people dance there. I'm not even sure if it still exists.
Jimmy Woo is a welknown place - never been there, but I guess it's solely dance music and probably hipster. Then there's Bitterzoet, but I don't know what they do for club nights either. I only know it from gigs but it seems like an ok place. I'm guessing it's fairly hipster during club nights though.
I'm not sure how welcoming the average mainstream clubs are to large groups of English males. "Brits on stag" do have a reputation in Holland and mostly it's like Phlegmscope writes above... I wouldn't be surprised if you'd get refused entrance in some places, while other clubs probably specifically cater to British stag-tourists. But Amsterdam's full of tourists in the summer, so you'll probably be okay walking into any random pub near Leidseplein or Rembrandtplein.
As for non-cultural daytime activities, a typical thing for Brits on stag weekend (other than the red light district, sex museum, Heineken brewery tour, yadda yadda etc.) seems to be renting a beer-bicycle. I sometimes see them in the streets. It's exactly what you'd think it is: a large bike with a built-in bar (bartender/driver included) on it. You can ride it with 15 people at the same time, do some sight-seeing through the city while listening to cheesy tunes, get drunk and randomly throw insults to innocent bystanders at the same time. Looks like it might be fun... Other than that, maybe renting pedal boats to go down the canals could be fun too? I dunno.
Places to eat - again I can't really help you very much. If you're looking for Dutch food, I guess poffertjes (little pancakes) are a typical Dutch cuisine that I enjoy (although I never eat them). Furthermore it's the time of the year for fresh herring (yuck!) and there are various traditional Dutch dishes containing cabbage and stuff. Chips with mayonnaise and kroketten (greasy meat snack) is very Dutch too. You'll find lots of places where you can get Indonesian or Surinamese food too, which is probably better than the native Dutch food.