1. What's the most cost effective way to improve the system?
What kind of music do you listen to? No point in recommending some accurate yet bass light speakers if you're into D&B, and likewise no point recommending floor standers with masses of bass if you only ever listen to classical music! But from the sounds of the rest of your equipment, would recommend speakers before everything else. But as RichPenny says, seperate pre/power amps or bi-amping can make a good difference.
2. What's the best way to connect an iPod to it?
Eeeesh. You've spent loads of money on HiFi and you want to listen to low bitrate MP3's on it! 😕
If it matters that much, just buy any old iPod dock that connects to the amp via phono connectors… Or re-rip all your music on your computer as WAV's, buy a half decent external USB/Firewire Soundcard with inbuilt 16/24 bit DAC (look at Tascam probably) for about £100-150, then connect it up to your amp… Oh, and buy a MASSIVE hard drive for your computer before hand as most likely you'll need the storage space!