Your system sounds good. In terms of connectors, I assume you are referring to cables from MX Electronics. It might be worthwhile changing this to an established brand such as Monster, QED, etc. You can also try DAC Cables from Mumbai.
FLAC is good, though an IPOD will not recognise and play that format. If you are good at computers look at the free Exact Audio Copy for ripping your CDs. It is a little difficult to install and run, but once you cross that initial step, it creates exceedingly good copies from an audio CD.
Down the line, you should look at something like a Squeezebox to interface your PC to an independent audio system.
In terms of a CD Player, the easiest choice and one suited for your amp will be the 540C CD Player from CA.