I can't remember exactly what you're up against in Hell, but here are a few general tactics you should use in a situation like that.
First of all, Jon Irenicus brings four demons with him and lets them do the fighting while he runs to the bottom of the map. You can't see him do that because he's using Mislead. I think he has two illusionary forms--one beside the demons, and one to the east. The first thing you should do is to concentrate your attacks on the demons. When they are dead, you can fillet Jon Irenicus at your leisure.
True Seeing and True Sight will dispel the illusions, and you can get to work on the real Jon Irenicus on the south side of the map. I can't remember exactly what protection spells he uses, but you need to dispel them. Also, in the Slayer form, he is resistant to magic and he regenerates hit points. So you need to hit him hard and fast when his defenses are down. When his Slayer form is destroyed, you'll have to fight him yet again in his human form.
As in any other combat situation when fighting a Mage, pay attention to the spells he's using, and tailor your attacks accordingly:
- If he's using Spell Turning, take down his protection with Secret Word, Ruby Ray of Reversal, Khelban's Warding Whip, or Pierce Shield. (Breach, Pierce Magic, and Dispel Magic won't help.)
- If he's using Mislead, take down his protection with True Sight or True Seeing.
- If he's using Stoneskin, Fireshield, Mantle, Improved Mantle, Protection from Magic Weapons, Protection from Normal Missiles, Absolute Immunity, etc., take down his protection with Breach.
- If he's using Spell Shield, take down his protection with Ruby Ray of Reversal, Khelban's Warding Whip, Pierce Shield, or Spell Strike. (Breach, Pierce Magic, and Dispel Magic won't help.)
- Dispel Magic might help against protection spells that can be dispelled with Dispel Magic, but if the difference in level between your characters and the enemy is too great, it won't work. Only a 26th Level Mage or Cleric or an Inquisitor 15th Level or higher can dispel Irenicus's magic effectively (since an Inquisitor casts Dispel Magic at twice his own level).
As you can see, you can cut through Irenicus's defenses if you use the proper spells.
To protect yourself from his attacks, Spell Immunity helps your Mages. (Protection from Necromancy is probably your best bet.) If I recall correctly, Irenicus summons an Efreet and casts Sunfire or Fireball, so protection from fire (spells, potions, or items) also helps.
My memory of the event is somewhat distorted because I just played BG1 last month where the monsters are easier to deal with, and before that, I played Throne of Bhaal, where the Mages make Irenicus look like a chump. The last time I fought Irenicus in Hell, Imoen was 28th Level, and she singlehandedly mopped the floor with him (and scrubbed the tub and toilet, too). I don't know how much higher in level your party needs to be before you can defeat him, but if you have nearly finished the critical path and a couple of major side-quests, you should probably be okay.
However, I think it's a shame that you missed so many side-quests in Shadows of Amn. You can't go back and do them when Shadows of Amn ends and Throne of Bhaal begins. I don't know if you have any saved games (it would be a shame if you had to start over completely), but you'll probably be alright no matter what you do.
Good luck!