Did your guinea pig get pain medication?
It sounds like you are doing the right thing (hand feeding lots - www.guinealynx.info/handfeeding.html) It sometimes takes a while before they can eat on their own.
The vet gave metacam for the pain but said to stop using it now and to continue with the emeprid until the bottle is empty, we have stopped this also as his stools are still a bit loose at times, Do you think this is correct to do this?
Could the hair loss around his eyes be stress from the bullying?
Do you have crisp clear pictures of the hair loss around the eyes? Are they watering? It could be fungal or from wetness.
Continue to watch for signs of pain though he may be fine.