I received an 800 on Math L2 and 740 on Chem, but also a 580 in Physics and 660 in Bio M. I’m honestly not that terrible at either subject (took both AP classes, received As and 4s) and since most of the colleges to which I am applying do not use Score Choice, I am thinking about retaking both tests in October so colleges see that I have improved (hopefully.) Is this a good idea?
Also, if anyone could recommend good Physics or Bio prep books, that would be greatly appreciated 
No. You have 2 very good scores. Colleges that ask for 2 scores, even if they do not use score choice, generally say that they look at the 2 best. At some point, you just need to take colleges at their word. You time would be be better spent polishing your essays.