Questions on the five Skandhas
Rupa


  Does this refer to physical form? 


Yes, anything physical is included in this category. Ex: light, sound, aromas,earth element, water element, heat element, air element  etc. 
However, with regards to the five skandhas, a thought is also called a rupa when it becomes the object received by the mind sense faculty. Ex: a memory


  Can we only know form through the sense organs?


Yes, there'll be no knowing without the 6 senses.

Vedana


  Are these just sensations from the sense organs?


Sense organs cannot produce sensation by themselves. The contact should occur. That is the union of Rupa, sense organ and the relevant consciousness.
ex: light, eye and the eye consciousness 

There are basically 3 kinds of sensations: pleasant, painful and neutral.


  If this is the case, does emotion fall under sensation?


No, that is Sankhara(Mental Formation).

Sanna(Perception)


  My understanding is that the faculty to recognize is consciousness


No. Consciousness is just base awareness.


  how is perception and consciousness different?


Sanna(perception) is what recognizes the object specifically. Awareness cannot tell what it is. But awareness is present at this stage as they all rise together. 

Sankhara(Mental Formation)


  I'm assuming this is where emotions exist? Is happiness an emotion? Is
  loving-kindness an emotion?


Yes, that's right. Happiness, loving kindness, hatred, jealousy, craving etc. belong to this group

Vinnana(Consciousness)


  If this is the case, then is consciousness that which observes
  sensations, mental formations, perception and form, or that which
  experiences sensation, perception, mental formations and form?


A single experience contains all 5 of the Skhandas. They make up the whole experience. Think of it as drinking a chocolate milk shake. When you drink it, do you feel the taste of milk, chocolate, sugar separately? No. You feel them all together. Consciousness is like the water they are all mixed in. Consciousness cannot separately observe anything. Observing itself is an experience where all 5 skandhas are present.  In an experience, consciousness simply plays the role of being aware. When you are asleep, the ear consciousness may not be present at the ears. That's why you won't be able to hear, even if the sound hits the ears.


  Can the experience of sensation exist if we are not conscious of it?


No. Every experience has all the 5 skhandas. 


  Are animals conscious?


Yes, they are beings. It's Panchaskhandha for them as well


  what is the difference between consciousness and self-awareness?


Consciousness is what plays the role of being aware in an experience. Self-awareness is an experience(5 skandhas) in which the perception identifies the object of the experience as a self.   

To give a common example to illustrate the functions of the Skandhas, say you are smelling something delicious. The smell and the nose here are Rupa. When they get together with the nose consciousness, contact happens. At that moment the Vinnana is aware that an object is present at the nose sense door. Vedana tells that it is pleasant. Sanna tells what it is: whether it's a pudding, cake, ice cream etc. Sankhara tells it's good and desires for it. Keep in mind that the event of smelling here involves many instances of five aggregates rising and passing away.