I recently completed the AQ40 scepter chain on my main (bored out of my mind really) while doing about 1/2 of it on my shamans. I found:

MC is a joke, you can probably solo this instance with a geared 80. I actually take 15 mins a week now and kill garr/baron to farm bindings, got 1 binding so far on my pally. It took me about an hour to clear the entire instance when I needed a book for my AQ scepter, I'd say Baron Geddon is probably the hardest boss in there (I fight him in the tunnel and spread my team around so they don't hit each other, my pally de-magics people rapidly). If you have a direbrew remote you can port over and head into MC from brd within 5 minutes -- jump through the lava.

BWL is tough, I couldn't get past the first boss as a 5 boxer. You have to MC razor (so down to 4 ppl), and adds stream to him and the person MCing. I think with practice its definitely 5 boxable, but bleh. I got some friends help with him, then they left and I 5-boxed the rest of BWL no problem. Did wipe on drakes and nef a few times but got it done eventually, easier just bringing in friends/pugs. The trash is more annoying than bosses, just face the drakes away from people and I used pally bubbles to temporarily remove debuffs (the drakes are 10x easier if you can bring 2 tanks).

ZG and Karazhan and ZA are jokes, I farm the first boss in kara every week for mount (got 1!) and the 2 ZG mount bosses every 4 days (0 mounts qq). Just all tank'n'spank.

I had to spend ~20 hours farming the first trash pack in AQ40 for rep, I tried the first boss and as you found out the MC is brutal. I actually found it easier just to do it solo on my prot pally, got him down to 10% and then self-wiped since I didn't want to save to instance. On my server there are dozens of old-world pugs that run weekly, and they all love multiboxers.