Could I number my works cited sources and put them in my in-text citations using (1), (2), etc.? Just wondering because I used a lot of sources and my paper would look a lot cleaner in my opinion. I'm using MLA format by the way.
MLA is essentially a two-part system, with author-page parenthetical citations referring the reader to a bibliography of “Works Cited.” Discursive notes (with superscript calls in text) are allowed over and above that, but not to replace the basic function of citing sources. There are documentation styles that can and do operate much as you say you want to. These are associated primarily with the hard sciences, and include CSE (Council of Science Editors) style. But if your editor or professor has asked for MLA that really is not an option.
Generally, if you prefer to use numbers to reference citations, it is best to do them in superscript in the form of footnotes (look at any Wikipedia article).
As far as numbers in parentheses, I'm not certain, although it shouldn't pose any problems as long as your bibliography is clearly numbered so as to make the association obvious.