The latest version (v22) of Sword Coast Stratagems is compatible with BG:EE.
This is a BETA release, and I mean the beta label fairly seriously. This version merges the BG and BG2 versions of SCS, adds BG:EE compatibility, and rewrites most of the code base. The chance that I broke something in doing this is fairly high. I hope to release a non-beta-labelled version in a couple of weeks, depending how much feedback I get for this version.
EDIT: Updated to version 23, though I think I'll leave the beta flag in place.
EDIT: Updated to version 24 (not before time). This version fixes the problems with Davaeorn, Mulahey and Bassilus that have been reported, as well as bringing the "NPCs wait at inns" and "allow NPC pairs to separate" components to BG:EE and playing more nicely with the BG:EE text strings. Still technically a beta, though I'll probably strip that label shortly.