I am so sorry for your loss. I would bleach (30:1 ratio) all of the runs and let it sit for at least 15 minutes before rinsing. I would also bleach all of the common areas. Make sure all volunteers wash their hands before handling different dogs and be sure to wash door knobs and other things that you touch very thoroughly. Wash food bowls, water dishes, etc. in hot water and the bleach solution. Do a search on infectious disease control for shelters. There should be good information on simple things you can do to prevent the spread of disease. At our shelter, we use infectious disease protocol all of the time because incubation periods can vary and even dogs/cats that appear to be healthy can carry disease. We always bleach kennels before putting a new dog in them. I always recommend that volunteers also change their clothing and wash before handling their own pets. I even wear different shoes while in the shelter and I do not wear them home.
I understand how hard it is for shelters. All I can suggest is that you network...network...network...flyers alone probably won't do it, but you can use the Internet to contact different breed rescues in and around your area. Contact them BEFORE you need to solicit their help and ask them if they have any suggestions on how you might be able to work together in the future. Don't think inside the box because many organizations have national outreach or contacts in other areas...it is not out of the question for a group in the midwest to help on the east coast, etc...don't assume, always ask...At our shelter, transport saves lives that would otherwise be lost because of low adoption rates locally. It takes time to build a contact list, but it is a priceless investment.
Advertise your available pets on Petfinder. Ask local newspapers to do a pet of the week ad for you...many do it for free. Many radio stations have to do a public service announcement, so solicit interviews with them and the local media. We also put up flyers in local veterinary clinics. Those folks are a great resource for soliciting potential adopters.
Fundraisers not only raise funds, they also raise awareness so get your group out into the public eye and ask for help. Hosting seminars to teach the public about animal health, training, grooming etc. usually go over very well. Many veterinarians, groomers, and trainers are happy to speak at these events for free.
There are also grants available for shelters...recruit a volunteer to help with grant writing...
Ask local businesses to contribute. For example, our local Wal-Mart donates all broken bags to the shelter. Sometimes veterinarians or pharmaceutical companies will donate meds or deeply discount them. The bottom line is that you cannot be afraid to ask.
I know that managing a shelter can be overwhelming...I served as President of the board for one. There is a common problem that many shelters fall into the trap of focusing all of their resources on the day to day care of the animals and neglecting the advertising, education and fundraising tasks. They barely have enough volunteers to keep the kennels clean and the animals fed...you have to be resourceful and constantly recruiting.
Sorry if I sound like I'm on a soapbox. I've learned a lot in my years of shelter work and I'm always happy to share ideas, sometimes too happy! Good luck & keep the faith!