I see where the problem lies - looks like I may be doomed to use Alt+M on all the books. Turns out the one thing missing from the filenames that would make calibre recognize Title/Author is a simple dash (eg Title-Author). I used a renamer in the middle to get rid of abnormal characters since the site I use to backup my books doesn't accept abnormal characters. Thus, renamer got rid of the dashes that calibre recognizes as separating Title from Author.
I guess the only question I have left would then be: Is there a way to change the regular expression from (?P<title>.+) - (?P<author>[^_]+) to something that would recognize the Title+Author without the dash?
I tried (?P<title>.+) (?P<author>[^_]+) expression (same as earlier but without the dash) and it ended up only getting the author's last name in the Author field, while the first name remained in the Title field.
Thanks for everyone who's been helpful on this one