About the URL format of uploads: a little mod could be made, for SMF to interpret them as well. The relevant code is in parse_bbc() (Sources/Subs.php).
About the links rewriting, I think a solution would be a .htaccess file which would rewrite on the fly exactly as you say, the URL with topic.asp into one SMF-like v- that is, would redirect the user to the new one, when he/she clicks on the old one. (assuming your server runs Apache or something accepting .htaccess files and mod_rewrite is enabled)