I've sent a whole bird for necropsy by the state, prepped and sent by my local vet, cost was around $140...$35 vet, $105 state. The state did not do a full panel test and did not give me a satisfactory answer as to what was wrong. I then took another live bird to another vet (a personal friend of mine who is on the state list of avian vets). He took blood from the live bird and sent it to the state...I'll have to see if I can find the cost tomorrow might have been $65. He put the bird down and did a necropsy for me at no charge. I think he made recommendations to the state lab as to what to test for and they came back with a diagnosis of Mycoplasma Synoviae. The symptoms my birds had/have is chronic diarrhea which causes egg peritonitis and the hen dies or they are weakened, get impacted crops and die. I have put some down due to fly strike also caused by the diarrhea. The other main symptom they have is the head shake...mine seem to do it in response to noise like if the cocks crow or I talk to them.
I had the birds, that brought the disease here, quarantined for 8 weeks but did not do a good job of it I guess as my original flock became infected. I'm pretty sure it was from not changing my shoes between coops. I don't remember how long it took to infect the old flock....maybe 10-12 weeks?
Because you don't know what you're dealing with it's hard to say if you should save or cull. I culled 70 birds, cleaned the coops and let them sit idle for a couple months while I got some hatching eggs to start over. Hatched 7 last fall and bred them this spring...hatched 40 chicks. I'll be butchering everything off again this fall as they all have the head shake/diarrhea. I plan to clean/disinfect everything again this fall and let it all sit birdless over winter to see if the cold will kill the disease off....I'm guessing they may have been infected by the contaminated ground around the coop or maybe my compost pile.
Some just cull sick birds and bury the dead when it happens but I enjoy breeding a good bird and this summer the enjoyment is not there because some of them are sick again. I just had to cull one of breeder hens for egg peritonitis... did a home necropsy and she was just filled with infection. She was the best typed hen I've ever had and I'm quite disappointed at this setback. So depending on what might be going on with your flock you might just cull and/or breed for resistance, cull/clean and start over, or maybe vaccinate. There are many pros and cons to each choice...the decisions will need to be what's best for you.
Good luck!