So I've played through BG about 3 times, never finished BG2. I have a pretty typical playthrough going on my desktop where I'm playing as a divine remix kit cleric (fresh and fun) with Imoen, Jaheira, Khalid, Minsc, and Dynaheir. I changed Minsc to a barbarian and bio to describe him as a former ranger etc and changed dynaheir to a sorceress, more fun and makes some sense.

Now I'm starting a separate playthrough for a pure fun experience but canon enough to meet might OCD needs. I plan to use the mods: BGT, Divine Remix, Rogue Rebalancing, Kit Revisions beta (only affects fighters right now), Tweaks/Fixes, and SCS 1/2. I find the game doesn't feel quite right without Jaheira and Khalid (especially transitioning to BGII but frankly their classes can be quite boring. I was wondering, with shadowkeeper what are the best class/kits to make the NPCs and which NPCs should I take with me. Also, any additional mods I should add would be appreciated.

Using Shadowkeeper, i'd change Khalid to a Berserker. Of course, for rp purposes that's plain silly, but in the early stages Berserkers are easily the best tanks in the game. If you couldn't care less about roleplaying, make Khalid a raging berserker:)

Jaheira is fine as she is (though it takes some time before she gains momentum). Optionally, you can change her to a ranger/cleric, which will give het access to both the druid and the cleric spellbook.

As for other mods, i'd use SCS 1 and 2, which vastly improves enemy AI (the AI is dumb as nails in the original game). Obviously, this also makes the game far more challenging.

As for the other NPC's: i'd take along Imoen and dual her to mage at level 7, after maxing lockpicking and traps. If you don't mind memorizing a few Knock spells, you can dual her at an earlier level. Just make sure she has Find Traps maxed, since a couple of traps in Durlag's Tower require a (nearly) maxed Find Traps skill.

Minsc and Dynaheir are the obvious choices for the last two spots. Make Minsc a barbarian and give him proficiencies in 2h Swords and bows.I'd change Dynaheir to a sorceress. Give her a ring of wizardry and she can cast magic missiles all day.

L1NPC lets you change your allies as you describe. I've gone through and altered all of them to some extent.
BG1NPC gives you more banters, which I think makes the game much more enjoyable.
Item Revisions and Spell Revisions changes items and spell effects, most of which I agree with.
SCS gives opponents better AI, and can make certain areas MUCH more challenging. Challenge is good, yes?

Poke around Gibberlings3, Spellholdstudios, Pocketplanegroup and Sorcerer's place(?) for mod ideas.