1) Would it be a good idea to finish vanilla BG at least once before adding the ToSC expansion, or is it an issue not worth worrying about?
IMO, it's not worth worrying about.
2) When multi-class chars level-up, are their hit point increases limited by their most restrictive class, or does each class-level-up use their own innate hit dice?
I've never played tabletop AD&D, so I don't know the rules regarding this. My *guess* that they use the hit dice of whatever class just leveled up. 1d10 for Fighters, 1d8 Clerics, 1d6 Thieves, and 1d4 Mages. Then apply Con bonus.
My new half-elf mage-cleric leveled up to a level 2 cleric. With a constitution of 16, she has a +2 hit point level-up bonus. So, is an increase from 8 hit points (what she started with) to 13 hit points, a pretty good level-up, or is it only mediocre?
Looks like she rolled a 6. Good, IMO.
I decided to live with the 13 roll, and have gone on with the game, but would like some clarification on this before future level-ups.
At first I re-rolled HP rolls, too. I stopped because I got *really* sick of reloads. Reloads killed the fun factor of leveling up, so I decided to let the fates decide. (This really bit me in the ass in IWD. I've got a mage who's rolled only 1's and 2's for of her HP rolls. Keeping her alive is an adventure in and of itself!) It keeps the game a bit more fresh to have the randomness. I also make it a practice to not use unidentified equipment, even if I already know what it does.
3) How effective (or ineffective) are two-handed swords?
Korror handled the weapon mechanics very well. I myself haven't really noticed a *big* difference in 1H > 2H (or vice versa) in BG1. A shield can be nice, but some of the two-handed swords are also quite nice - like Spider's Bane or whateveritis from later in the game. There are some decent 2H swords to make a party member proficient in it worthwhile.
Just delving into other weapons a bit: Good spears you practically never see. The same goes for good Halberds. And I am just plain not fond of crossbows.
However, it did occur to me that if you wanted to use a 2-hander, you could keep a bow in a quick weapon slot, and not have to give up using a shield, like you would have to if you wanted to pair 1-handed sword use with a bow.
Sure, that works fine. Shoot at stuff before it gets in close. 
4) Multiple guides I've downloaded have mentioned that Imoen starts the game with a wand of magic missiles. I've never seen that with any of the characters I've taken out of Candlekeep...
She has it when she walks out of Candlekeep and joins up. It looks like a little pink flower. If you don't have it try patching (or installing TotSC).
5) I had the impression that in BG, once you removed an NPC from your team, they disappeared from the game, and couldn't be re-recruited. One guide I read said you could remove Minsc if he started getting impatient, rescue Dynaheir later, at your convenience, and then re-add Minsc to your team. Is that true? If so, does it only apply to these two, or other pairs, too, or even single NPC's?
If an NPC leaves your team (alive) and they did NOT hate your party, they'll stay where you left them if you need them later. Sometimes even if they do walk off, returning to the screen later will find the NPC in the spot you departied them.
I don't know if departying them when they're complaining about their personal quest will send them off into the sunset to quest alone. I'm thinking it probably won't. Generally speaking, I don't think you should run into problems with this. You have ample time to do the quests. (I believe the time period is anywhere from two to three weeks. Rough guess though. I always did the quests promptly.)
6) Alright, now for the most complex question - what to do about the roster of my new team.
IMO: Go with people you like. It makes the first trip through more pleasant.
With the prior team I referred to, I had Hesperia (a half-elf mage-cleric), Imoen, Montaron, Xzar, Jaheira, and Khalid, until Nashkell. There, after Montaron and Xzar left (or were booted out, I don't remember which) I added Minsc and Branwen, and was more or less content. Unfortunately, I didn't move fast enough for Minsc's taste, and he kept going postal. After about the tenth time he attacked the others, I gave up and killed him, out of frustration. Ummm, yeah I maybe could have handled that better...
Hm, seems you didn't have ample time to do his quest - or waited way too long. Anyway, the Gnoll Fortress is quite a deal easier with Minsc with you. His racial enemy being Gnoll, pitting him against one is like putting a carrot in a Cuisinart. So, I'd recommend jetting off to rescue Dynaheir right away - Minsc should handle those bipedal hyenas with ease. But remember: rescuing Dynaheir means you'll need to have her join you. Maybe losing Minsc was for the best in the instance you mentioned, but I seriously question whether you were RPing your alignment if you butchered him like that. :p
However, later I added Ajantis, and that wasn't a bad team either. Anyway, I was still clearing sectors around Nashkell when I decided I needed to do something different for a while (Jaheira had reached level 4 as both fighter and druid, I remember).
Oh, indeed. Ajantis is a *great* character. His Detect Evil skill is excellent for getting a rough idea of the number evil critters on unknown maps.
This time I decided to do things a little differently. ... poor Xzar died tragically in a skirmish with bandits, valiantly attempting to help his friend Montaron by attacking a bandit with his dagger. RIP.
So... so cruel...
Then Iolanthe added Khalid and Jaheira, and started clearing the sections along the way to Nashkell. However, in Beregost, I suddenly decided to have her dump Montaron and add Kagain (hadn't tried him at all before - he's better than Montaron, though quite a grump).
Kagain's great. He regenerates HPs. Hell, I think he heals even when traveling between maps. But he's not necessarily good for your party. Conflict can be fun, but you might prefer a more cohesive party.
Kagain ... already occasionally grumbles (being Evil). According to the manual, at rep 16 he quits being "Unhappy" and becomes "Angry" - "Breaking" at rep 18. So maybe I should just let him go now, add Minsc, and tackle the Nashkell Mine sector, heading for Dynaheir soon after.
Removing Kagain would be a good move if you plan on high reputation.
Still, could Ajanatis and Minsc (with occasional help from, probably, Branwen) be enough of a front-line complement to get through the game?
I don't see why not.
Don't like that idea, so who could I add? There really aren't many other non-evil fighters in the game. The only ones who appeal are Coran and Kivan (both of whom I've heard some people like).
Yeslick. He's middle-to-late game, but Yeslick is a strudy little bugger. You could replace Branwen with Yeslick at some point, giving you a sturdy fighter/cleric to help battle alongside Minsc and Ajantis.
So, is it practical to go with a 5-person team for a while, or is it feasible to go from the Gnoll Stronghold directly...
Both options are feasible. And remember, unless you go off to parts unknown (e.g. Basilisks, Durlag's Tower, Ulgoth's Beard) you'll be battling mostly Kobolds and Bandits through the next few chapters. Two fighters should be able to handle that.
[o: *LEMMING* :o]