Everyone has their own methods for tuning a vehicle. Whether it is carbs, aftermarket fuel injection, or even stock injection in plain Jane form or slightly modified.

What sort of processes do you guys do for tuning? What methods have you done, what has NOT worked for you?

I'm looking for info from humbling personal experienes here on examples of what lead you to blowing something up, catching something on fire, etc, please stay on track.

Not sure if this is what you're looking for, but when dyno tuning, I have a general sequence in which I set everything. Assuming everything is ballpark, I always tune the airflow first. This includes intake venturis (length and size), valve sizes, cam selection, and exhaust headers(length and size). This, of course is usually pretty tied down to engine design with little or no room for adjustment, unless you get creative (as I like to do). After that, it's all ignition timing. Get that curve right for the flow characteristics that you just established. Find optimum total advance first, then play with your curve characteristics if possible. Finally, fine tune the fuel mixture.
Again, you should be in the ballpark from the test bench, and verify that you're in the ballpark in the first couple runs. The last thing you want is to burn a valve on lean mixture while on the dyno, because you haven't gotten around to trimming your AFRs yet.
Also, this is obviously a very vague MO, but it should work for any internal combustion engine. It comes from what I've read and what I've mulled over in my dome at night, and it's all based on making changes in an order that won't detune what you've just tuned. And when you're a budget racer paying $60hr for dyno time, it pays to have a plan that gets you out of there ASAP. Hope that helps.
Mark D.

Wow, thank you. That's some good info, Mark!