I've been looking into this myself because I plan on using my computer as my source. As long as your cds are in good shape(no scratches or smudges) and you rip to .wav or a lossless format, then the files should be an exact duplicate of the cd.
Many people use EAC to rip there music to .flac. I downloaded it the other night. It's very simple to setup and it will even give you a percentage of how closely the ripped file is to the cd. However, I think I am going to use iTunes and rip to Apple Lossless since I prefer to use iTunes as my jukebox.
The reason you may tell a difference between the cd and the files on your computer is not because they are of different quality but because of the path from your computer to your amp. If you use a cheap or built-in soundcard, the quality will not be nearly the same as using a dedicated cdp. Now a more expensive soundcard may be a step up, but you will likely still notice a difference.
One way to go about it is to get a soundcard that has digital outputs(coax or optical) and connect it to an external DAC and then into your amp. You could also get an external DAC that supports USB in which case you would just connect your computer using a USB cable. The DAC1 is one example of this and everything I have heard about it has been very good.
I just purchased my first stereo setup(my amp is arriving tomorrow) so I am very new to all of this. For now, I will just be connecting my soundcard directly to my amp to begin with because I am not ready to spend $1000 on a DAC1. However, I am looking into a cheaper dac. I have read good things about the Beresford TC-7510 MK-5 but they have stopped selling them because they are about to release the a new MK-6.
As far as a remote control goes, you have many options to choose from. I'm pretty sure ATI sells an IR remote. You could buy a Squeezebox 3 which comes with a remote and connects to your computer through your network. Another option is something like Salling Software
which allows you to use a phone, palm pilot, or pocket pc as a remote for your computer.
As far as distance between your computer and your amp, if they are in separate rooms, you could use something like the Squeezebox 3 which connects to your computer through either a wired or wireless network.
I hope this helped some. I'm very excited to get my system setup, so I've been doing alot of research.