This is interesting and something I will pursue with the USDA. I did tell them about our "group" and that many others may be interested in this depending on what he means by bleeding my birds. I hope he just means a normal blood draw! I will let you all know what I find out.
Thank you for contacting me about potential MDV field isolates. I would certainly be interested in receiving samples from backyard flocks in addition to commercial flocks. Are you able to bleed the birds yourself or have them bled by someone else? Do you still have the 3 unvaccinated birds that you didn't lose with the first 6? Isolating virus can be a challenge and our best chance is from birds that are visibly sick, but if your vaccine is currently giving protection, then the next best alternative would be the unvaccinated birds or the serotype 3 (HVT)-vaccinated birds.
Regarding your other questions, if you want to know the virulence of the virus strain, pathotyping is about your only option. It is unfortunately a long and laborious process, so we're only able to do a handful of field isolates each year. Results can take 4-6 months from the time the samples are submitted. PCR testing will only confirm that your birds are infected which is likely the case if it was confirmed by necropsy. MDV vaccines protect against developing disease, not infection. Also, it is very difficult to distinguish between virulent MDV and CVI988 vaccine by PCR. The vaccine in the link you provided is not commercially available. That vaccine candidate causes lymphoid atrophy in maternal antibody negative chickens which prevents regulatory approval. Current research is being done to try and prevent this problem.
If you're interested in sampling I can provide instructions.