1. What do I do with money? And why should I worry about a big economy if I can't rush buy units/buildings until way into the game?
If you run the Universal Suffrage civic, you can hurry production with cash; the rest of the time, you use it on espionage, diplomacy (buying techs, resources, attacks, peace, whatever) and to run at a higher than sustainable slider setting if you're CE.
That is, on higher difficulty levels you'll often have a negative yearly gold income because you want to have your research (or other) sliders up high; the "invisible money slider" is then at 10, 20, 330 and often doesn't earn much. If you're awash in money it may be a Chieftan/Warlord issue where the game's just a bit easy in that respect. You might want to go 100% research if you aren't already and get Universal Suffrage so you can use the money for production.
2. Unhappiness seems to be an issue and slavery solved it temporarily but not longterm. I wasn't really going for any particular victory type, although I did build anything religious or cultural that popped up.
http://forums.civfanatics.com/showthread.php?t=189559
is a helpful article about the different ways you can get happiness. A very big one is developing and hooking up any luxury resources you have. Some require buildings to function, some don't. + culture and + happiness are different things by and large; a Monastery doesn't provide any happiness and a theatre only does if you're running the culture slider >0 (which is unusual) or if you have access to dyes. Another big one early is military units if you have hereditary rule running as a civic.
3. How do I focus on religion, or can I? In my mind I envision creating massive amounts of missionaries and spreading my religion throughout the world. But I don't know how this is accomplished in the game, and if it is even helpful or not.
Assuming you want to found one yourself rather than conquer a holy city, you rush the techs which enable a religion and hope you beat the AIs to them. Once that's done you either build a monastery which produces missionaries, or run Organized Religion which enables missionary production anywhere. Then you send out your missionaries like you mentioned. Also, the holy city has a chance to spread the religion on a random per turn basis along its trade routes, with the odds per turn increasing the closer cities get to the holy city. Building your holy city's shrine (1 per religion) doubles this random spreading and also gives you coins for each religious building of its faith, including those in other civs, making a shrine a nice economic boost with a well-spread religion.
4. Victory conditions. There seem to be a lot, but I'm ahead by 400 points or so and not sure what I need to do to "win."
Well, all it really means is you save your high score; I actually turn off everything except conquest and play as long as I like, then just retire. Without knowing what your empire looks like it's hard to say whether Space Race, Conquest or Diplomatic would be easiest. Basically, set up victory conditions based on what you want to do in the game, or else a range of possibilities you might want. (Basically, whether or not you want diplo, religious, cultural or spaceship wins to be possible needs to be decided from the start.)
5. How do I change which specialist is being built?
Specialists aren't built as such. The most 'normal' specialist is a worker that's been taken off of the city's tiles in the city screen, so that instead of working the grassland cottage or whatever, there's now one guy in your specialists section; what kinds of jobs he can have depends on your civics (caste system allows you to run as many of whichever sort) or on buildings - a library, for example, allows 2 scientists.
6. What is it okay to automate and when is it not? I've had mixed results from clicking on automation, mostly good when going all out production. (OMG everything takes SO long to build or research for the first several hundred years, though).
I wouldn't really advise it. The habit of building everything in each city is a key one to break, and you usually know best whether a city is going to be for commerce, production, or specialists.
When you start the game your production queue will look quite inaccurate because you'll have a city size of 1; if the city is going to grow to 3 long before the "50 turns" or whatever is done, that number is pretty meaningless. It's generally dogma that "worker first" is the way to go with cities even though it actually -does- keep your city from growing. (Warrior first is hardly a bad choice, workboat first can be better [city still grows] and expansionist civs may want settler first.)
7. I'm used to grouping three units into "armies" in Civ:Rev, but that doesn't seem to work here. How many of a unit is considered the equal of say a Civ:Rev army of archers in each city for defense?
Haven't played Rev. I think 1-3 units is a normal city garrison unless you're using hereditary rule to tamp down a lot of unhappiness; it's situational. A lot of the fighting in Civ4 tends to involve a big army in one 'stack' - they aren't killed off all at once or anything and they choose the best defender if it's attacked. These are often called "Stacks of Doom/Death" (SoD) particularly those belonging to the AI.
8. Workers on automation to build roads, improvements and trade networks rock.
Sorta. As the levels go up it becomes more and more vital to do the upgrades exactly in the order you need them most. Good decisions early on bear compound interest as you play; so getting that worker out a turn sooner matters, getting him to start improving on the same turn as he moves matters, having agriculture or animal husbandry researched just in time matters, etc. Try to avoid wasted worker time and prioritize what the city needs most (often food right at the start.
That's all I've got for right now. My head is still spinning from the hours I wasted last night. Reminded me of the old days. Guess it never stops being addictive.
You know, I'd almost written off 4x games as a genre that'd had its day, like adventure gaming, but Civ4:BTS is brilliant.