I am 1/2 through the same problem and since I have many obligations and have not yet found a way to use an assitant, it hs taken abut 18 months. It is going faster and each work session gets more efficent. Here are my suggestions.
First, have faith and be persistent, try to do some thinking up front and end each work session postiviely, not in exhausted frustration. You can do that by literally writing a step (next action) that is so clear you know when it is done, like "process today's mail per GTD" and "process first one foot stack of recent stuff". Do try to work in 30 minute segments, use the first 5 to hink and warm-up and the last 5 to note your progress and highight what worked.
Second, here are some suggestions:
Brain storm your categories first. It is easier to set up a bunch of folders first and then start sorting. However, you will "discover" and create some as you go along. There are probably many alternatives that would work so don't sacrifice "good" in an effort to get to "best" at the start. Think about what you need your papers for and that might help you also. Be sure to write out the outcome you desire for the project first --this should be a short sentence not a mission statement. You may have sub-projects and defered projects (SDMBs). If you have sub-projects you maybe treat them as projects and just keep the overall project as your goal, as it is too big too do. Make sure you have a huge trash receptacle as you want no physical impediments to trip up your mental energy's flow. Set up your basic system. GTD suggests A to Z only but this did not work for me, but you should avoid complex hierarchies and file heads that are supposed to trigger your thinking-all that could be in a list. My suggestion here is not really GTD but it is working for me. Get as many bankers cartons as you think you will end up with, given the situation and the space available. You will need at least 6 (probably many more) then label one each as follows. Business: Financial, Business:Personnel, Business: Customers, Business:Reference and Projects. Within each it would be A to Z. Personal/Family:Financial, Personal/Family:Personal Documents and Essential Records (label folders by last name and expect to need 3 to 4 for each person as you will have documents like birth certificates and passports, education, health records, and maybe wills. Finally, you will have your own general reference file. You will also need a box, cabinet or container for office supplies that are hidden in your piles. Band-aides, hand lotion, and a labeler help. But, if you do not have labeler, use a good marker like a Sharpie (get a box of them), they have a way of disapearing.
In the event that you find that you are stuggling with what to file something under, take a folder, cut off the front and write the file head and then "See ___".