Doing it my way, or am I misleaded?

Hello,
I am a newbie when it comes to blogs.
I do know XHTML and CSS pretty well and enough PHP/MySql to understand globally how WordPress works and not to be afraid to tweak it here and there.
Don’t get me wrong, I don’t know much about WordPress, I only downloaded it a few days ago. And I must say I find it hard to get the information I want. It may very well be that I’m not looking at things the right way.
I want to use my current design (blog independent) which is 100% valid XHTML1.1 & CSS. I wish I could have WordPress output XHTML 1.1 but I could settle for 1.0 strict.
My idea is to simply use function calls I find in WordPress files (like index.php) and incorporate them where appropriate in my own file(s).
It seems simpler to me than having to work around the current index.php or wp-comments , etc. I already have a solid set of CSS files and like my naming convention.
I hope I am clear enough and you can tell me if this would be totally crazy (counter-productive) or simply not viable (future-proof).
Thanks.