If my understanding of your situation is correct, did you return to Littleroot at any point to speak with Prof. Birch and register him in your PokeNav? In any case, I've put out a patch that prevents interacting with Birch from blocking out Looker. However, for your file to work properly, I'll need to edit it manually so that the Rocket Quest works as is.
I'd love to hear what strats you used and what fight was the most tricky!
Much less creative than my original E4, honestly - the battlefield conditions were intense enough that it really did feel like I needed raw stats and coverage far more than anything else. A big part was figuring out how to weave in 2 layers of toxic spikes on each fight. For Wallace, I actually save-scummed for a double protect because the only way I could come up with to cook the fight was:
1. Lead Tox/Ray, lay toxic spikes, swap Ray to Aegislash to tank double ice moves
2. Bunker on Tox (poisons Poliwrath), Toxic Kyogre with Aegislash
3. Bunker again on Tox, swap Aegislash for Blissey
4. Second layer of spikes on Tox, swap Blissey to Aegislash to null Close Combat from Poliwrath
5. Bunker again on Tox
Then the next turn Tox usually dies, but that ensures that almost everyone gets Toxic applied. Palkia and Gyarados are a bit of an issue, but it's fairly manageable, and eventually Kyogre thunder cleans up.
As far as fight difficulty, I think Wallace might have actually been the hardest with this setup. Phoebe second, probably. But figuring out how to set up under the Kyogre/Poliwrath gun was a fun puzzle!
One thing that was fun, actually, was TM-ing in the middle of the E4 to replace Dragon Pulse on Ray with Flamethrower for the Glacia fight. I couldn't figure that one out until I realized I could just... add a fire move.