Let me answer my question:

Once you start SoD, all your companions continue with the same level and same equipment, including everything in their inventory.

After you finish the prologue, the following happens:
- canonical companions spread around
- their inventory goes into a chest (but not their equiped items)
- some canonical NPCs will meet you again in SoD, Captain Crowin will tell you their locations, e.g. Khalid, Neera, Jaheira, Viconia, etc.
- some I couldn't find yet e.g. Alora. It seems like she is not making an appearance and her equipment is just lost
- custom companions (i.e. those you create if you choose to start with a party instead of a single character) just wake up next to you, with all their equipment intact, ready to party up

So, by far the most convenient choice is to use custom companions.

I did fiddle with EEKeeper to figure out a way to keep Alora and it seems to be quite easy too. Go to "Miscelaneous" and set her Script, Override Script and Class Script to "NONE". She will be treated as a custom companion and carry over.

First off, my apologies for writing a wall.

When you finish BGEE, you immediately start off with your entire party in Korlasz tomb equipped and carrying the same inventory in their backpack with the possible exception of Imoen. If she was in your party in BGEE she will be there as an observer but will not join your party. Safana is there and can be recruited if you need a thief to replace Immy. If you have another thief of any type then Safana won't be there.

All of Imoen's equipped items will be placed in "her" chest on the top floor of the ducal palace which where you end up when finished with Korlasz' tomb. So be sure to go to the other end of that floor before finish that part of the game. Her backpack inventory will end up in "your" chest on that floor.

HOWEVER, nothing she is carrying/equipped with is available to you when in Korlasz tomb. My first run through of SOD I learned the hard way and had to do without a couple of helpful items she had. I got them at the palace but sure could have used them. So be sure you transfer anything critical Immy has (gem bags, scroll case, wands) before you finish the final fight in BGEE.

Now, any character in your party in BGEE will come with you and help in Korlasz' tomb. BUT, when that is finished your party splits up. Anything in their backpack will transfer to "your" chest in the ducal palace. Anything they are "equipped" with stays with them. Not a big deal for those you can recruit later in SOD. If the party member is NOT available in SOD then that gear is gone. So before you leave Korlasz' tomb, make sure you unequip any items you want to use for SOD from your party members. There is a dialogue with Imoen to finish the tomb so it won't happen suddenly.

The following BGEE characters will be recruitable in SOD:

Minsc & Dynaheir - immediately after finishing Korlasz' tomb
Safana - also right after.

Chapter 8
Viconia, Edwin, Rasaad, Baeloth

Chapter 9
Jaheira, Khalid (can be recruited separately now), Neera, Dorn

The following NPCs appear but cannot be recruited:
Garrick, Coran, Tiax, Skie

These NPCs will disappear after the tomb and do not reappear:
Xzar, Montaron, Kivan, Kaigan, Branwen, Xan, Shar Teel, Eldoth, Quayle, Alora

EDIT: You posted while I was typing. I think I covered anything you hadn't figured out .

Thanks for the reply.

Everything you wrote is also written in the wiki. What nobody talks about are the custom companions.

They carry over normally, don't disappear and they are by far the most convenient choice.

There is also like 3-4 new companions you can find in SOD, though none of them seem to carry over to BG2.

Originally posted by Holysword:

What happens to custom companions (that is, the ones you create if you decide to start EE with a party instead of a single character), will they be gathered in some tavern somewhere or are the lost in EE?

The good news is they just come along with you. Custom characters always do. Now for the bad news. In the final chapter, when it all becomes cut scenes, any custom characters just die! I would suggest you kick them out before you rest in the castle. A good idea is to export them at this point, so you can later import them into BG2 (with their gear.)

Also, SoD does sometimes have issues with Mod NPCs. I have had them break the game in the first dungeon. Also, the game treats them as "custom" for purposes of the final chapter. Just FYI.

Thanks. I didn't mind the spoiler, and that was good to know.