First, I'm really sorry to hear about the misfortune you have had over the past several years. I know how things can pile up on one's emotions, and my hat's off to you and your family for even surviving all of this without a total meltdown.

Secondly, while I am no expert on this, here's how I would approach your task that feels overwhelming at the moment. I would set up empty plastic tubs or cardboard boxes all around you, sit on the floor, and just start one-by-one going through everything. After 12 years of stuff, you might find that much of what you have can be purged, so be sure you are familiar with the records retention rules associated with your business. Some records are only required to be kept seven years, others for the life of the business, etc. Label your tubs by business, including one big tub for trash. Then just start sorting. Once you have everything sorted by business, then it may not feel so overwhelming to go through one business at a time. By then, you will know that everything in there needs to be kept and filed, so you can then start with the wonderful Smead products

to establish your filing system by business.
This may take a while to do, but you can at least feel good once you get the first business files set back up into a manageable form, and then you'll be inspired to do more. Especially when all the paperwork is cleaned out and up-to-date and you know it's necessary. What a wonderful feeling that will be!
Good luck, and I hope 2010 is a much better year for you!