I made this basic A10 Warthog model in blender that’s supposed to have different parts (like elevators and ailerons) rotating based on the actions you perform flying the plane. When I import the model in Unity most of the parts have messed up rotations and position coordinates how do I fix this?
Unity ver: 2017.1.0f3
Blender: 2.78
Ahhh your pivot points are off man. Heres a couple of tips:
So Im assuming all these seperate parts are all seperate objects, so first of all press ‘shift+c’ to zero out your 3D cursor. Next, go to each seperate object, and zero out their pivot points, do this by selecting all the objects (you can do them all at once) and pressing ‘alt+ctrl+shift+c’ and selecting ‘Origin to 3D cursor’. This will set all of the objects pivot points to 0,0,0 on the x,y,z.
This may cause any issues if you have any mirrors on, but I’m going to assume you know how to sort that out, if not, hit me up. 
Now, making sure once again yu have all the objects selected, go to File>Export, and export as an FBX. In the settings you want to make sure you have ‘Selected Objects’ ticked, and the scale toggle deselected, so it should look like this:
This will bring all the objects in together, but dont worry! They are still seperate! They will all just be parented under whatever the last object you selected was (I suggest the planes base).
Alternatively! You can export them out one by one after you’ve zeroed them out as seperate objects, and import them thusly. When you go to drag them into your scene, make sure you drag them directly into the hierarchy. If you do this, with them all zeroed out correctly, they should all line up, if they dont or you just want to make double sure select the piece and make sure its x,y,z location in the inspector is all set to 0,0,0.
Then just group them under an empty… or eachother… whatever, and you are set to go. Make a prefab of that baby and go nuts.
Hope this helped. 
Edit: Oh one other thing I noticed looking at your pics one more time… you may want to drag everything back so its lined up with the 0,0,0 in Blender as well, looks like you have everything back by the tail, the more centered is the easier it will be to work with in Unity.
Thanks for all the help! Everything is now working as it should.
Ahh! Thats awesome to hear, happy I could help!
This helped. though I also have an issue with the faces flipping
Blender always having bugs.
Many faces? Or just a few?
Yeah. And even Maya too.
