I noticed that the recommended way to delete the cobwebs and the old funiture is to use the "Markfordelete function. This requires lots of patience and trial and error. Instead, it's much easier, less time consuming and safer to simply delete the parentref of the said objects: open the console and type "df495.disable" (without quotes). The house also looks much cleaner than with the markanddelete function as it also gets rid of the mist and some other effects.
The above is applicable after purchasing the house via cheats - console commands: "setstage a7b33 10" "completequest ms11" "completequest ms11b"and then purchasing the upgrades from jorleif (make sure you purchase the "clean the mess" upgrade before all the others).
If you didn't purchase the "cleaning" upgrade first: type "df492.disable" : this will get rid of the bloody mess.
(the getparentref console command can be priceless to find the parent object controlling the status of the children objects )
To remove the "Investigation targets":
Near the bloody chest: d55f2.disable
Near bottles and broken glass: d5625.disable
Near the pots in the kitchen: d5662.disable
Near the altar with skeleton: d57f6.disable
Front of wardrobe with hidden door: d57ef.disable
In the upstairs bedroom: d57f7.disable
Near the small bookcase with the butcher leaflets: d572c.disable
Near the other wardrobe and the small bookcase: d57c7.disable
Also, I noticed that the dialog with Jorleif to add furniture to the small room which is almost in front of the master bedroom in the Windhelm house was also not showing up in my game. If you have the same problem, open the console and type:
df496.enable
df497.enable
Edit: apparently getting the housecarl fixes this last issue with the "guestroom" but I'm leaving the codes just in case..