I have the same problem with a forum of mine. Previous this last update/algo change I had about 700 pages indexed in Yahoo. site:www.example.com gave me about 600 in Yahoo and 700 in Google. Now I have about 33 indexed in Yahoo...My traffic dropped with 40%. The new Yahoo SERP are dominated by spammers.
Do you have back links from other sites, if you do they point to the main domain url only.
If not, get other sites to link to you to the pages other than you main URL, if you have subdirectories better to link to them than just individual pages. Try to get them on topic from the sites that rank well and/or in Yahoo Directory Sites.
Check 302s on your own site, if there convert to 301 redirects.
Example of 302 on your own site could be a shopping cart page action.
Avoid linking with sites that are not indexed properly or scrappers. Before changing everything do analysis on your link structure. Get an advice from someone else.
Be patient. - It helped me a lot getting re-included.
I have the same problem with a 9 month old site that has dozens of 1 thru 10 listing in my desired key phrases, but much of my quality content resides one level down in a sub directory clearly listed on my site map page, same top level domain, and no tricks. Just an extra /widget.htm and Y won't crawl it.
I have also linked interally to several /widet.htm pages but no results. I am consitering tearing the sub dom dowm and throwing the 50+ pages in the root.htm to see if it solves the problem, but I really dont want to do this.
Slurpbot hits me like mike tyson, so I must doing something wrong.