Not happy yet

Your Cd player has a retail used valur of 40.00.
How much money do you have to spend.Forget the cables.Dont even consider this untill you have put your last available $ into a CD player upgrade.
Once you have listend to the system for a month or 2 them its time to see how much money you have to take the next step and go from there.
One other thing,you need to put a heavy area rug down.Need to tame the room slightly.
Dont try to do it all at once.One component at a time and slow and easy.

You will have to experiment, but what you describe can sometimes be caused by dirty AC power. Try a AC power conditioner. Ones that work well for not too much cash are: Monster HTS2000; Vansevers Super Companion; Audio Power Pack II; Panamax 1000. My favorites are the Vansevers and the Audio Power.

Much as I hate to agree with Thunders....he is correct. You have three things that need work.
The CD player should be the first and most expensive. Whatever you get, you probably want to keep for a while.
I suggest a 24bit HDCD player, or a good DAC if you prefer that route. The room you describe is hell on good sound. You might want to follow leaf's recommendation for a large area rug and bookshelves or drapes or something to help with the walls. Last would be the cables. Start with ICs. I don't know your speakers. Your Pre is made by a company whose Amps are great but there are better preamps in my opinion. Rotel is a solid performer for the price.

You may be able to improve your bass performance with speaker placement. Try pulling them away from the wall.

Thunders,Leafs,Snooker have some good points, as do others.
Lets not go overboard, or make too many changes at once,
but here are areas that need immediate attention.

1)Your CD player is really holding you back, there are no good Yamaha CDPs, since you have Rotel amp look for good used CDP here with 24/96 dac, like Rotel 991 which can be had for $600 used here. Also used Musical Fidelity A3CD,
Link Genki, Audio Refinement, Roksan Kandy/Caspian, Rega Planet and many others would make a huge improvement

2)Your interconnects, speaker cables, AC cords must be upgraded to better cables, the good news is there is huge selection of great used cables for any budget here at Audiogon. This will make a huge improvement, there are so many choices requires a seperate topic.

3)Very important to minimize room colorations/distortions.
You must put area rug (Persian or Turkish my preference)
between your listening seat and speakers, bare wood floors
are not good for music. Also place something in both corners of speaker wall to control sound distortions, large plant or decorative item. If your speakers are 6ft apart try to sit 6-8ft from speakers for best sound.

Keep the current preamp/power amp and speakers till these other areas are addressed.