Are any of the wattles swollen? Or is it the spaces between the eyes and nose, and the eye areas?
Are the nodules at all like scabs? I wouldn't vaccinate for pox at the moment as you might have asymptomatic birds who, if being vaccinated with pox while actively fighting it, will be overcome.
Never vaccinate for ANY illness while the illness might be active; that goes for any disease. Wait til it's done and then vaccinate the ones that were asymptomatic.
IF wattles are swollen, I'd look seriously at pasteurella. Otherwise, several respiratory illnesses include swelling of the face as the general sinuses are inflammed, filling with the products of immune response.
HOwever, nodules. This is a key symptom. First thing I would want to do any time you see a nodule is open up the mouths of the birds and see if there are corresponding whitish or yellowisn nodules or cheesy patches in the mouth/throat.
If patches, along with external nodules, I'd suspect diphtheria (wet pox). If nodules, I'd at the least suspect hypovitaminosis A (A deficiency) with a corresponding primary or secondary respiratory infection/symptoms.
I would treat ALL birds immediately with vitamin A, and not the water packets. Water packets aren't very effective at all for the oil vitamins (A, D, E, K) and A and E are very important in this type of illness, A being particularly important. You can try treating the flock with the water packet and just watch them carefully, and the two ones inside with polyvisol (4 drops daily in the beak - one week). IF you want to flock treat, then you can either get liquid cod liver oil or fortified wheat germ oil (horse section, feedstores) and spray with a mister-type sprayer, handheld garden sprayer or smaller cosmetic sprayer (kept in a dark place or light proof). You will spray that on the top of the new feed twice weekly - no more vitamins than that, no more often than that. DO it first thing in the morning, and make sure to take up their food the night before so that they're eager to eat the top layer quickly before the light gets to it.
Of course, all birds should be eating a good completely fortified ration, age appropriate. That means a crumble or pellet as 95% of their diet. Check your feed - make sure it's within a month old, kept in a dry, light-proof, moisture proof, container - n ot a bag. Vitamin A easily degrades from dry feeds as oil vitamins really need oils/fats for best absorption/storage.
If it's not a vitamin A deficiency, the vitamin A supplementation temporarily and in these small amounts will help with mucous membranes (the eyes' edges, the respiratory system, etc) and their healing, the E will help with inflammation issues and acts as an anti-oxidant against products of the pathogens (viral, bacterial, whatever they are).
I would be prepared for flock treatment with antibiotics. Tylan soluable seems the best for flock applications. The mycins and cyclines aren't advisably strong any more. A flock that large, you want to hit this hard and with a good antibiotic that covers a lot of the diseases.
Get it to have on hand to have at your disposal.
In the mean time, VetRx used as a swab for the nares, roof of inside of beak, etc will help the birds with swelling to breath past their inflammation, which might be partially aleviated by the VetRx.
In the mean time, yes - quarantine. Remember to do those two birds last in the day after the main flock. Use different shoes and a covering shirt when you do them - leave them with the sick birds. I find that antibacterial hand gel used after handling the sick birds' utensiles, etc, helps prevent me from spreading germs on the doorknobs, etc, when I leave their area.
Make sure they drink! If that means adding a little liquidized honey to the water, do so. (I mix honey in an equal amount of nearly boiling water - stir til cool and liquid, add that to my waterer). Also yogurt wouldn't hurt the sick birds or the well in case they have any sinus drainage - prevents secondary bacterial/fungal enteritis. You can still use yogurt if you use the Tylan soluble.
I hope this helps.
In the mean time, if you could please tell me their exact diet, where they live (barn run, free range, etc) and what their bedding is, any recent changes, etc?
Thank you!