6 months ago, my sites were having trouble in Yahoo, most likely because I had too many affiliate links, and not enough content. Or, I had too many outbound links in general (not necessarily “affiliate” links). I was suffering from the penalty where Yahoo shows only your main page in the index, and then as a sub-result, it shows the same thing.
Anyway, I increased the amount of content on my sites and didn’t do anything at all with the links. A few months later, my sites were indexed properly. 
In your case, I suppose it could be due to duplicate content, depending on how much is actually duplicated on those 40 pages. Check out this duplicate content / similar page checker — it might be useful to you.