I've managed to get Longer Road, the mod that allows Irenicus to join your party in ToB, working with BG2EE. Couldn't have been simpler. Download the mod from here: http://iegmc.shphockey.com/longerroad/LongerRoad_v1.5.1.zip
and extract to your BG2EE directory.
Open setup-longerroad.tp2 in notepad.
Comment the "REQUIRE_FILE" lines near the top by adding "//" so that they read:
//REQUIRE_FILE ~Data/25Dialog.bif~ @2
//REQUIRE_FILE ~Data/25Scripts.bif~ @2
Now install! You'll know it's working if when you start a new game of ToB, Ellesime almost immediately appears to talk to you. Just to be safe, don't click the stone heads until she appears.
You have to have a combined INT+WIS of 24 and choose the right (slightly odd) dialogue options with Ellesime in order to get a necesseray tem. Note that Irenicus is hilariously OP. He's a level 30 mage with with an item that gives him +4 spells at every level, +1 INT and permanent haste. He also has innate immunity to petrify and charm and reduced casting time.
Please note that I have only playtested it up to the point when Irenicus joins. I'm actually playing through SoA right now so won't be testing further until I've got to ToB. I'm playing with SCS, Tweaks, Atweaks, BP Ascension, UB, Kelsey and Banter Mods. I installed Longer Road last. One of the mods I have prevented the Longer Road music from installing but no other problems that I can see so far.