Headunit: Havn't heard the Alpine or Eclipse unit, but I do have the Nakamichi CD-400 and that unit is AWESOME. Sound quality and clarity on this unit is amazing. I can hear every little detail, can picture the size of the recording studio/auditorium based on the amount of echoing on the vocals, and the unit is extremely quiet (almost no hissing/noise). Very well worth the $300. My previous unit was the JVC SH909 and although still a very good unit for its price, was nowhere near this CD400 in terms of sound quality and clarity.
Speakers: I'd have to go with Infiniti Kappas Perfect also, they sound clean, soft, and warm and aren't overpriced. But if you go big, get the CDT Eurosports.
Amp: Phoenix gold or Alpine. Both are excellent amps. Or go big and get yourself a hybrid tube amp. I have the Tube Driver Blue 2-channel amp and it sounds so ****ING NICE.