It's more complicated than just buying a new window. The window panel is sewed into the bottom of the top at the well, IIRC. So you will need to have a complete new window panel installed. As for cleaning the top, here is an old thread on the subject:
http://forums.vintage-mustang.com/forums/showflat.php?Cat=1&Board=forum&Number=172911&fpart=1&PHPSESSID=
http://forums.vintage-mustang.com/forums/showflat.php?Cat=1&Board=forum&Number=172911&fpart=1&PHPSESSID=