It annoys me that a shop that no longer has an owner has all items marked as 'Steal'... is there a way to unmark these? (Without the use of console commands?)

no

You can sell them to a fence and buy them back.

http://elderscrolls.wikia.com/wiki/Stealing

Well, there is.. so.. shush.

Wy tank oo.

Launder it by selling it to a fence and buying it back

enchant it IIRC

• Selling the item to a http://elderscrolls.wikia.com/wiki/Fence. When the item is sold, the flag is removed, and you can buy the item back. However, this method can be very expensive. Stolen items cannot be sold to regular merchants. The items will not even show up in the list of things to be sold when you open up the merchant window. Stolen items can only be sold to a http://elderscrolls.wikia.com/wiki/Fence.

• Returning the item to the owner. Due to the way http://elderscrolls.wikia.com/wiki/Stealing# handles stolen items, the stolen flag is only applied when the item is taken by someone who is not the owner. The flag is removed when the item is back in the possession of the owner, such as in the owner's body. Taking an item from a body does not count as stealing, though you most likely have to have the owner's body available before using this method.
  
• This method does not always work in houses where multiple people live and places with merchants, because of how the interior area ownership is handled. Merchants have their items flagged as owned by 'someone else' to prevent them from being sold by the merchant, while multiple-resident housing simply has messy and unclear ownership.

• Enchanting the item. By using a http://elderscrolls.wikia.com/wiki/Sigil_Stone or an http://elderscrolls.wikia.com/wiki/Altar_of_Enchanting, you can http://elderscrolls.wikia.com/wiki/Enchant the stolen item and it will become a new, un-stolen item. This only works on armor, clothing, jewelry, and weapons.

• Mix the item into a potion. Potions made from stolen ingredients are not considered stolen.
  
• Deposit the item into a chest then have a follower steal from a chest, then trade... when you take back the stolen item the stolen flag will be removed.

Pulled from TES: Skyrim wiki. http://elderscrolls.wikia.com/wiki/Stealing

This may sound stupid. But do i have to join the Thieves Guild to use their fences?
Are there no fences that do NOT belong to the thieves guild?

If you don't plan on making money from them, sell to a fence, or merchant in a separate hold, and buy them back. (useful if you stole a weapon or armor you want to use). But if you want to make money I wouldn't worry about it, you can just sell to a fence, or to a merchant in a separate hold. I think fences pay more too.





If you don't plan on joining the thieves guild, you can sell a stolen item to a merchant in a different town, from witch you stole it in. Fences pay more, and you cannot use a fence unless you enter the thieves guild though.

I attempted to sell to Belethor (the stolen items are from Windhelm) but he isnt having any of it

I'm really surprised that wasn't a high level Speech perk.

That's very odd. I sell tons of my stuff to him. I wouldn't know then. Other then the thieves guild. To use their default Fence you just have to do their initiation quest though, so it takes like, 5 minutes.

Speech perk allows you to sell stolen items to merchants you have invested in.