IMO, you shouldn't focus the specialization of your cities making difference between gold and science cities. Gold and Science cities are both commerce cities, so they're basicly the same thing (remember, commerce isn't the same thing as gold in Civ 4; commerce is something you can transform into gold or science depending on your slider). If you're going to run your science slider high, gold buildings aren't going to be effective, since the base gold in wich they'll add their bonus isn't going to be high (e.g. if you're running 80% science, only 20% of your commerce will become gold).
But, if you can spare the hammers, there's no problem in building the gold buildings (specially markets and grocers, since they give good bonuses to happiness and health, if you have the resources needed).
You mention that the capital under bureaucracy should be focusing on gold. Remember that the bonus from bureaucracy isn't on the gold produced by the capital, it's on the commerce. So, if you're teching by using a high science slider, capital should focus on science buildings first, IMO. Other important thing to notice is that you need 6 libraries and 6 universities (on standard size maps) to be able to build Oxford Univesity (100% more science in one city, very nice if you can get it fast), wich is one of the best National Wonders in the game. So, it's better to build libraries and unis first.
The only thing I'd call a "gold city" is if you happen to have a city with a good religion shrine or with a good corporationh HQ (merchant specialists also give straight up gold, not commerce, so a city running a lot of merchants could be a good "gold city" too). This buildings produce straight gold, not commerce, so they'll benefit from gold improvements even if you happen to run a 100% science slider. Normally a city like this would be the one where you put your Wall Street. If you don't have one of these, I'll probably put wall street in the city wich produces the most commerce that isn't going to build a better National Wonder.