If it's truly a virus then you'll have to get every rat on antibiotics. Everyone would already be exposed and it would be "too late" for immunities. I know when hopefloats was hit with one, she had all rats on 2 (actually might have been 3) antibiotics and a steroid. I'm sorry you lost Milton, RIP cute boy. <3
Viruses don't spread like you're describing though... two deaths over the period of months are not likely a virus.
Viruses ravage through colonies and wipe out large numbers within a week or two.
For general immunities, I find children's echinacea drops (1 per day, you give it for a week then go off for a week then back on for a week, etc.) work well.
Here's where I got mine, a bottle will last a lifetime haha:
http://www.vitacost.com/childlife-echinacea
Also, I've heard good things about Booster, which I have used but we weren't using it for immunities in particular.
http://www.exoticdvm.com/Omega3Booster
Is the Booster I have, I was given it for Rocky because of the Omega 3 specifically. All of my rats seemed to love it, although like I said I can't say in particular that I ~know~ it did much for immunities.
Do you have a HEPA air purifier? That might also help.
What temperature do you keep your rat room? A lower one is better, more towards 69 degrees Fahrenheit.
A good diet and healthy weights always help too.