Hold your horses and be patient - most Eos owners have no intention of selling their cars especially those that have been properly cared for and maintained.
You will find cars that have been thrashed, trashed or accident-damaged without too many problems - not a good buying proposition for obvious reasons. MY07 and MY08 models will be more common as many of these may not have been fitted with the later modified seals and will be prone to ongoing water leaks unless the owner goes to considerable expense to have the modified seals installed by an experienced Eos technician as discussed elsewhere in this forum.
The limited numbers of Eos vehicles delivered in most countries makes it difficult to find a significant number of vehicles offered for sale at any particular time and it may take you a year or more to find the car that meets your expectations especially when you restrict colours and options required.
Long-time members of this Forum may recall my prediction nearly 6 years ago that the Eos would become a modern classic and this request confirms this is beginning to become evident as buyers with specific requirements enter the market following the announcement that production is to cease in the immediate future and a replacement hard-top convertible is unlikely. The next indication will be the price of pristine used MY09 and later Eos vehicles increasing as collectors and enthusiasts compete for the limited number of such vehicles that will come onto the market in the years to come.
"Everything comes to those who wait - some just have to wait longer than others to be in the right place at the right time."
We used AutoTrader to find our EOS. AutoTrader has a very good search options box where you list your 'desired' options. However, it also tells you how many cars are listed for sale with those or other options and you can play around with your choices.
You are searching for a used EOS in a limited and diminishing market. From those search results you can get an idea what the most popular options are. Using color as an example, we found black EOS's the most common, but there were only 6 at the time in Leoni blue/beige that we wanted. We traveled half way across the country for our 2007. Do the same for automatic DSG and manual transmissions. You will find more manual options available.
Unless you have a lot of information on a used EOS history from a private seller, consider paying more from a genuine VW Dealership, but watch their extended warranty because it may not include roof leak problems.
Your features wish list seems a bit strange. We got a Tdi (manual) 'Sport version' and later I wished I had a highline version with inclusive features like cruise, HID lights and radio steering controls. These are VERY expensive to fit retrospectively. When buying older used cars that have dropped a lot in price, consider the high end feature versions as you will get better value.
Knowing what I know now about potential DPF issues, I should probably have chosen a more feature rich 2 liter petrol EOS in the same color. But our Tdi in this heavy car returns 51 mpg touring mpg and 45 around town. The Sport Tdi also has less electronic complexity and looks nice.
I agree with Silvershadow on the Eos being a modern classic, I certainly have no intention in selling mine actually I did need mine for a commuting when I bought it was bought for pleasure only and I did buy it to use, I've done 18500 miles in two and a half years ownership and that is pleasure use only. I have a 4x4 that I have also owned from new 17 years ago and still enjoy it very much and have no intention of parting with that anytime soon either.