I vote you get rid of the Rotel stuff and get a nice integrated amp that matches well with your speakers. The Wadia/DAC magic combo is fine in my opinion.
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I have a Monarchy DIP 24/94 between my Wadia iTransport and my tubed CAL Alpha DAC, and there is no 'hard edge' to speak of (1m Kimber D60 from Wadia to DIP, .5m Orchid AES/EBU from DIP to DAC). Sounds like you've taken car of one of the main considerations in using your iPod as a source, i.e. importing music into iTunes using Apple Lossless format (and not as MP3s). My iPod sounds better as a source than my CAL Delta transport hooked up the same way, which makes no sense to me, but it is what it is.
Keep your eyes peeled for a used DIP - it won't hurt any, and if it doesn't work for you, you can sell it on Audiogon without losing your money on it.
i bought an adaptor from voodoo cable to allow for use of a better pc - lessloss -- and i also use an excellent digicable -- a kharma grand ref. i think a good pc and digicable will help tame your nasties. quite frankly, i have not heard any jitter issues although the itransport allegedly has high jitter.
I have a basic Benchmark DAC hooked up to my Wadia 170i, and the Benchmark driving two channels of a Theta Intrepid amp. Speakers are the Wilson Watt V's. All cables are high end, including a Kimber Select digital (RCA) cable. The combo is quite nice (I think the speakers are overkill, and cheaper priced bookshelves would work fine). The Wadia with an iPod is definitely high end if proper gear is used downstream.