Calibre/Kindle/PDF and illegal characters in Win

[Kindles]

I just recently got a kindle and started transferring my pdf documents to it. Since half of them has illegal characters (!, :, ? etc..) in their titles, calibre will automatically replace them with underscores so that Windows is happy. When they are transfered to my Kindle, underscores will fill up my kindle layout which doesnt look nice and proper. (since kindle read pdfs from its filename and not metadata which is annoying)

I was wondering if there is a way to configure calibre so that it will just remove ! ? from the filenames, and replace : with -?

Also, if I want to convert these pdf to mobi, is there anything i need to do in calibre beforehand? Any universal settings, or it's different for each?

One more thing, is there a built-in search function for metadata? Some of my books are not tagged properly and sometimes a slight difference in the title/author would cause calibre to not pick up the metadata from the servers. Currently I have to search on isbndb and then put the isbn into the metadata of the file so that it can fetch correctly.