Afraid of Upgrading to 2.9 due to Customization Loss

When I upgraded from 2.8.4 to 2.8.5, many of my customizations were lost and I had to laboriously re-do them. So now I’m reluctant to upgrade, because I know I’ll have to go through the process again.

These are the files that I’ve made alterations to which will most likely be lost once I upgrade:

• wp-login.php
• login.css
• common.php
• comment-template.php
• wp-comments-post.php
• comment.php
• wp-install.css
• default-widgets.php

Question: Is there any way to upgrade without upgrading these particular files? Or to upgrade them such that my customizations will be retained? Or to selectively upgrade only those files which contain “important” upgrades?

One way, of course, would be for me to simply copy these files as they are now, then upgrade, and then delete the 2.9 version of these particular files and replace them with my old ones. But then I’m not sure if the old ones will be compatible with 2.9, as 2.9 may contain some general re-structuring and may have consolidated or gotten rid of certain files altogether, and hence “mixing” versions may not work.