I had 2.1 and foolowed the guide on iClarified to upgrade to 2.2.1. I did a shift restore and everything. I thought that the whole phone should be wiped when i did that?
Now i have duplicate folders in /private/var/stash. Like two themes folders, two applications folders and so on. And other custom folders on the phone seems to be left unharmed also.
Which folders can i remove? They take valuable space.

It is an "old" iPhone 2G, right?
If so I would recommend to DFU restore to stock Apple Firmware 2.2.1 in iTunes and then use Quickpwn to jailbreak, activate, unlock. This way you'll get rid of the legacy stuff.
Just make sure after you used Quickpwn and connect to itunes the first time not to choose the option to "restore data from a backup", use "setup as a new iPhone" instead.
I would not recommend to just delete stuff, you never know which one is essential ;-)

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iPhone 3GS factory unlocked (3.1.2; Blackra1n, Cydia, OpenSSH, custom 3.0 ipcc file (no sig), tethering hack by Dev team, 32 GB)
iPhone 3G (3.0.1; Redsn0w 0.8, Cydia, OpenSSH) 16 GB