Hey guys,

I've just contacted the store, and here's the update.

The stains/stripes are indeed caused by a rubber guitar stand, it didn't have anything to do with the wrong guitar case. The store salesman didn't know these marks were there on the guitar.

But as he said it; there's a reason the guitar didn't sell, and was only sold with an "going out of business" sale price. Just take it or leave it.

About the case; this will probably have to do with the missing certificate. Someone took the wrong case and it isn't there anymore. Just like with the paint damage; can't do anything about it, all of this was included in the sale price.
(although he didn't know about any of this.)

As for the certificate: He will apply for a new one. This will come cost-free for me. Yeey!

And the receipt not showing a serial number wasn't a problem, the warranty will still be valid without the serial number mentioned on it.

So now the big question; did I got screwed? The advised retail price of the CS '69 Time Machine in the store was €3,799,- (that's $4,923,-) and I got it for €1,715 ($2,222)
It's a shame it didn't come with all the goodies, right case, and damaged paint, but it plays like a dream and sounds so good... I don't feel like I got conned, but what do you think?

Also, what are your opinions about upgrading it with the 5-way switch? Should I go for the bigger sound range, or should I keep it original?

Thank you all so much for helping me and thinking with me on this subject, as it turns out the stains weren't caused by the case after all!

Look at it this way whether it comes out or not you got a hellva a deal and almost 2,000.00 off also consider this saves you the trouble of giving the guitar its first scratch, dent or whatever. its a character mark.
Just enjoy.
Cheers