Welcome Danny
I would think your cables as long as they are in good shape and the proper size should be fine, and same goes for the cd player if its clean and in working order a new one probably isn't going to tame your top end...
It sounds like you want something warmer and more defined?
I'm thinking a speaker swap is going to get you the most change, something like the ascend sierra 1's but you will have to audition stuff to find out if it works for you... I don't have any experience with your bookshelfs specifically...
Another big change and what I would do if I were you is add a fast sealed sub and cross the bookshelfs to it, something like an svs sb1000 for $499, and then a pair of fmods to stop the lows from going to your bookshelfs, this will free up a lot of your amps power and give you more headroom for your bookshelfs, plus I notice when you have a robust low end the mids and highs seem smoother, kind of pulls them back a little.. For under $600 that IMO is going to make the biggest difference, I would start with some 100 hz fmods... Im not sure if you can accomplish this since you have an integrated amp, I know that rotel has preouts for the sub but I don't know how you would cross the bookshelfs before the amp section and not before the sub...
If that's not an option, I'm thinking a speaker change is in order, start demoing, there are a lot of decent inexpensive bookshelfs out there that are very capable...