The fact that only 200 out of a 1,000 emails are being pulled over may be due (this is an educated guess as I'm not familiar with Yahoo mail) to how Yahoo actually pulls your mail into your Inbox. By that I mean, it probably pulls and displays them 200 at a time. When you login and your Inbox renders, it probably displays your first 200 emails. When you scroll down to see your 201st email, it probably pulls the next 200. Easy Transfer is just seeing the first 200 and, therefore, only pulling those over. Make sense?
To get all 1,000 copied over, you might try this. After you run Easy Transfer, move the 200 emails that just got copied over from your Yahoo Inbox to one of your saved Yahoo folders under the My Folders section. Then run Easy Transfer again. Yes, it would require repeating it five times.. but it just might work.
If you decide to try this, please let me know if it worked. Thanks!