I'd say start over, like others said, and never allow homebrew ever, unless you have a very, very good idea of what it can do. If you don't want to do that, here's some pointers:
1. Note that AC is not the be-all, end-all of good defense. Touch attacks, area effects, debuffs, save-or-sucks, combat maneuvers etc. all work just fine, so use those some of the time. Really, there is no such thing as invulnerability in D&D. Even if you don't use the more specialized stuff all the time, AC 25 is far from unhittable. Even normal CR 4 critters can hit that on a 12 (Rhinoceros, Y White Dragon), 14 (VY Blue Dragon, Brown Bear, Griffon, Giant Crocodile), 15 (Giant Stag Beetle) or 16 (Owlbear, Minotaur, Tiger). That's not a bad chance, especially if you take flanking, charging, high ground, buffs, multiple attacks etc. into account.
2. Artificers need gold and downtime to be powerful, and can make good use of foreknowledge about what the party will be facing. Nerfing artificers isn't even required, but making sure they're not always in their comfort zone is highly recommended. Time pressure is an excellent way of making sure he won't get in your face with permanent buff items you didn't expect all the time. Another way is surprising the PCs with new and unique challenges from time to time. Also, Artificers live on items. There is stuff out there that covets said items, or just wants to destroy it. Thieves' guilds, Rust Monsters, sunder-focused Fighters, antimagic zones...
3. Gestalt effectively makes PCs two or even three levels more powerful than the number next to "level: " on their character sheet seems to indicate. Don't go all "Omigod, he's got AC 25 at level FOUR!". Coz that's only a number which doesn't say much in gestalt. Plan your encounters around CR 6 enemies being standard, easily killed opponents, with more challenging fights involving two or three of those, and you'll be fine. At this level, hitting AC 25 isn't really that big of a deal. It will happen.
4. Mix it up tactically. Don't go easy on them where the situation's setup is concerned, so instead of Ogres and Worgs on a plain, let them fight some Shadows in total darkness, dodging in and out of the walls; or have them rescue a damsel in distress from being drowned by some Kapoacinth under water; or stop some flying opponents from overturning a balancing platform the party is trapped on; or engage them with rat swarms in a labyrinth with sliding walls; etc. You get the idea, challenge not only their "numbers game", but also their tactical acumen and their ability to think on their feet.
5. The players are probably having fun with this one. So don't take it all away, instead let them have an easy(er) victory once and again! After all, that's what they expected out of the setup.
6. However, you can expect your players to work with you, too. So if they come up with truly game-breaking stuff, which even the community can't help you with, you're within your rights to tell them to tone it down. After all, it won't make the game more enjoyable for them if you're not having fun and are constantly frustrated!