Realistically, I'd estimate somewhere in the ballpark of 4,000, which is only slightly less absurd than your joke. From what I've heard, Apple stores typically only had ten or so gold units each available on launch day. That's what it was at the store where I was, and I've heard the same from others. Multiply that by the 413 Apple stores worldwide and... that's not very many. Pretty crazy.
I am sorry, but I think you are assuming a little bit too much here.
You are guestimating that 4000 gold phones were sold in the stores based on a 10 per store rumored number you've heard and 400 stores. Then you guess that retail is only 10% (another guess) and so multiply you original guestimate by 10 to get 40000 gold phones.
It's quite hopeless guesswork. We don't know the distribution of models in retail or online. We don't know how much is sold online compared to retail. We don't know how much was sold outside Apple's retail stores (by e.g. AT&T). We don't even know the geographical distribution (i.e. higher gold-ratio in China than US).
If we assume a factor 3 to 1 sales of iPhone 5S vs 5C based on Localitics'report (1), Apple has sold between 6-7 million iPhone 5S. Your 40.000 number isn't even 1% of that, so I think you are an order of magnitude off still.
Wouldn't be surprised if the bulk of the gold phones are shipped to Oriental countries, where the color is far more popular and sought after with much greater earnest (bordering on social imperative).
Purely anecdotally, a ton of the people in my line wanted gold, but only the first ten people actually got one. It seems plenty popular here too.
It will be interesting if we ever get a color breakdown to see if this "gold is for Asian countries" thing actually holds up, or if it's just another instance of bizarre cultural misunderstanding.
Other retail stores (Best Buy, Target, Wal-mart, cell phone stores, etc) got at least some shipments over the weekend, did they not? Perhaps some golds were included in those.
Extremely few. I doubt they got enough phones to make any significant difference in the overall numbers.
Totally anecdotally, I reserved a black (sorry, "space gray") phone at Target on Wednesday as a backup plan, in case I failed at the Apple store. They still haven't told me it's ready.
From what I've heard (hooray for rumors!) non-Apple stores are getting just a handful of phones, while Apple's stores are going through hundreds or thousands.