So as I walked around in Rorikstead and I picked up some wheat I noticed this old problem and wanted to fix it. I was surprised to see no-one has made a fix for it yet (EDIT: Unofficial Skyrim Patch contains this fix now), so I thought I might as well quickly make one for myself and everyone else.

What this mod does:

In vanilla Skyrim, when you pick up (harvest) wheat from various farms in the game, the left-over stuff remains about half a meter above the ground and not only does it look bad and sticks out, it is also clipped, meaning you can't walk through it (or over it), making it rather annoying.
I used the creation kit to manually move them all downwards so that they are stuck onto the ground after you harvest it.

As of now, I have fixed all the places with wheat that the Skyrim Wiki tells me of. These include:

Cowflop Farmhouse,
Hollyfrost Farm
Brandy-Mug Farm
Darkwater Crossing
Chillfurrow Farm
Battle-Born Farm
Hlaalu Farm
Loreius Farm
Fellstar Farm
Merryfair Farm
Lylvieve Family's House
Snow-Shod Farm
Katla's Farm

Version 1 only included these places:

-Rorikstead
-Solitude
-Dragon Bridge
-Whiterun
-Windhelm
-Ivarstead
-Loreius farm

If anyone somehow finds more that I haven't fixed or maybe some which I maybe didn’t place that well, please write the location in the comments section and I will change it immediately and update the mod. Other than that, the next time I’ll update is probably when a DLC comes out (hopefully not too much of a wait) if it has new buggy hay stacks.