I'm playing a character loyal to the Imperial Legion so I only started going to Windhelm after it was conquered. So I imediatly bought the house. On my way there, I see the victim of The Butcher which triggers that quest. I accepted to help, talked to the witnesses but I didn't care too much so I just went to my new house.

As I enter, I see blood all over, that's when I remembered that the house was also used for that quest. I investigate, talk to Giordano or whatever, come back to the house, open the secret door, get the diary, talk to her again, talk to the stewart and the quest's over.

I rushed through it because all I really wanted was a clean house. I take that opportunity and I immediatly buy all decorations. So I wen back, I go through the secret door and it's still a mess! Worse, I can't clean it up because most of the body parts can't be picked up. Blood is also still all over the place in the living room.

Did I screw up the house by the order I did things?

Yes, the house is buggy and you missed the step to work around it. You need to buy the clean up option from the steward before any other upgrades. And you should do it seperate, ie buy the clean up, check its done and then buy the upgrades.

atleast you got the quest in the first place, thats more than many gets :/

I've tried to move the basket with the skulls but now I spilled them all over the floor. Then I started kicking them to a corner but I just made it worse. What a mess. My wife doesn't seem to mind though. I guess I'll have to get used to the new decoration.

Yeah, you messed up a little. You have to ask to have the house cleaned up prior to decorating it. Unfortunately, if you don't you're stuck with the nastiness.