Yahoo is very slow crawler. Domain can have PR3-5 and only a few pages in yahoo index.
90% of webmaster work in google and yahoo with msn are additional traffic such as "bonus".
Why do you not count msn index?
Backlinks isn't also very important. Imagine domain with only 2 ingoing links but each with PR6 or PR7. Such domain will have PR6 and a few k pages in google index. But yahoo index... And your system give a few points for such domain
You can check PR of all ingoing links but it isn't real
Why do you cut number of indexed pages in google? If domain has 50k pages in index that domain has enough power of ingoing links for it.
One important parameter is outgoing links.
Best regards,
Wilson.