So I pulled the plugs and noticed that one of them, namely the left one, is kinda dark, while the one on the right looks alright. I ended up replacing both of them.

I notice that the bike is backfiring a bit more than usual when coming to a stop, there's a _lot_ more vibration, and starting from a stop seems more sluggish than before. Could it be that the left cylinder is running a lot richer than the right? Would that explain the poor accel and the almost unbearable vibration when it revs over 7k or so?

Thanks!

no expert here but when was the last valve job done....maybe outa spec on that side

I don't think it ever had a valve adjustment. I'm still waiting on kerry's kit, but I dunno who has it on the west coast 

is the vacuum tube from your petcock to the carb leaking gas into it?
mine did that and i couldn't figure out what the heck was wrong with it till i pulled that off and gas just pour out haha.

Went through the carbs - they seem fine. it's relatively new ('05), and from what I can tell, there's no damage or anything to the hoses and stuff. The only thing that could be wrong with it is the valves, since it's going on 5k miles and the valves still haven't been checked.

Also, this morning on the way to work I made the realization that at idle, the engine noise sounded really off, there was a ton of vibration, and a lot of unburned fuel was being spit out the exhaust. When I got off, the left side of the engine was a bit cooler than the right side (still hot to the touch though). Hrmmmmm... I wonder what's going on here.

Can someone describe what it feels like when a cylinder is not firing?

weel to me it sounds like the exhaust valve isn't seating all the way and the exhaust valve clearence shrinks between valve jobs so i'm still thinking thats the problem....for your idea pull the plug out and plug it into the boot/socket. Hold the metel side of the plug to the bike frame and have a friend give the bike a quick crank...if you see a "spark" then i don't think the cylender not firing is your problem....if you don't see one you found the problem obviously.

Check the fuel  levels in carbs. Carbs are all about right levels. If it overflows that gives you rich mix. The check procedure is straightforward. It's all in wiki.