Some time ago the company I work for has merged with another one and the website of that company was replaced with our content (absolute clone in structure and content). The main site ranks pretty well in Google while the clone is treated as a supplemental and has only several pages indexed. In Yahoo and MSN the situation is visa versa. The clone site (which is much younger) is in top 10 for all keywords, while the main site cannot be found in 500.
I'm planning to use 301 redirect. The question is - should I redirect each page one by one or the whole domain at once? The clone site's pages while being supplemental have have PR 4-6.

Thanks for any input.