It's just the bike's way of saying 'Honey, I'm home!'

The only way I found to eliminate it is to pull the choke out one notch before shutting down. It momentarily creates a super-rich a/f mix and eliminates the backfire.

The shutdown pop is half the fun of owning a big single!

One guy pulls the choke out and as he kills it lets out the clutch.

The problem is some fresh air is mixing with your exhaust gases which contain some unburnt fuel.  Once it hits something hot enough, kapow!

So, 3 ways to stop it.  eliminate the fuel or eliminate the air.  A very small air leak in your exhaust is enough to get a kapow.  It can be several places, head and header (check the gasket and retorque the bolts) header and muff (check the clamp and seal with a candle)  and all over the muff in case there is a rust thru.

3rd way, get a supertrapp.  I never get anything but a poof and I've leaned out the idle alot so that I get mild pops on shift.  

The header is dual wall and so is the muff.

check the holes on the bottom, leaks will show up here.  This knowledge is brought to you by our fellow members.  

I am also experiencing the "hit the deck,drive by" style backfire.  I've adjusted the mix screw a little and I can't tell any difference in the bike.  What should be happening.  I have an 86 with 18K and a Jardine slash cut.  The bike was a California model but a previous owner removed all the extra stuff.  Consequently I have lots of tubes under the seat that go nowhere.  The idle/mix screw cover was already off so someone previously adjusted it.  The other day i was riding and began to experience these weird hiccups/jerking as I took of.  It only clears up if I go at about 1/4 throttle or better.  Which way should my next adjustment go?

what was wrong with the petcock?

Regarding tuning the air/fuel mix:

Check out the article in the Tech section titled "Lancer's Straight and Simple Carb Tuning."  I read that thing over and over, and could never hear the engine changing speed.  Using the information he provides, though, I was able to get rid of my backfires.  Just do it the way he says to.  

When I finally WAS able to hear the engine change pace, I had just changed my pilot jet for a larger one.  Then it all made sense.    Just based on what I experienced, if you can't hear the thing changing, turn the screw out about three turns and run it for awhile.  If that won't fix the backfires, you either need a bigger jet, or the cause of the racket is something else, like an exhaust leak.

Sounds like ya'll are learning to "hear" the engine as you go through the tuning process.  It is easier to do if you have a tach on the engine, then you can watch the rpm change as you turn the pilot air adjusting screw.  As in the tuning instructions, you are looking for the highest rpm you can get.  If the pilot jet is the correct size, you should be able to find a "rpm high spot", and turning either left or right from that spot will decrease rpm.  If you find that as you turn the screw OUT (richening the mixture) the engine just continues to slowly increase in rpm until you get to 3 turns out, then you need to go to a bigger jet; start over and look for the "rpm high spot".  Whenever replacing a jet with the next larger size, it is usually easier to begin the process with the screw set at 1.5 turns out.
Then, with the pilot air adjusting screw set at the spot that your engine likes best, readjust the idle screw for proper idle rpm of about 1000-1200 rpm.