Yeah finding the model you want with the options you want can be a real pain, it took me a month to find the "right" used SLK55, which was located about 1,000 miles from me. It was still worth it though, even with the enclosed shipping cost since it was basically like new for 20,000$ off MSRP.
Anyway, back on topic. I actually test drove SL55, SLK55 (among many other cars) for several hours before deciding to go with the SLK55. My budget was 70,000$ or so. Here's how they compare in my opinion:
Interior - The seats are more comfy in the SL, more GT-like. I thought the SLK seats were more supportive and really hugged you in the corners. SL seats were a little too big for me and the visibility wasn't as good as SLK. The SL is a huge car... which isn't a good thing in my book. Interior materials were slightly better in the SL, especially the dash, but overall, all Mercedes interiors are high quality and there isn't a huge difference. Airscarf was a big plus in the SLK as well.
Acceleration - Pretty much even up to 60mph, both around 4.3-4.4 seconds. By 100mph, the difference is about 1 car lenght and by 120mph, the SL55 really starts pulling away. if you look at 1/4 mile times, SLK55 does it at around 12.7 and SL55 at around 12.5. At highway speeds, SL55 pulls away. Basically: from a stop, its even until 100-110 and SLK55 can overtake the SL55 if it has better traction. From a 60mph roll, the SL55 will pull the SLK55 without a problem by several cars up to 120mph and continue gaining.
Handling - SLK's superior handling is what made me buy it. I had a lotus elise before, so SL55 made me feel like driving a boat. There was way too much understeer and bodyroll, SLK was much more nuetral. You can really feel that SLK is 1,000lbs lighter in the corners. Steering and brake feel/feedback is much better in the SLK. As far as the brakes, I thought the SLK55 had stronger stopping power as well. Overall, I would consider the SL55 a GT and SLK55 a sports car.
IMO SLK55 was more fun to drive than SL55, so I got an 06 for around $53,000. I knew that 360hp wouldn't be enough for me after driving the SL55/SL600, so to fix that gap, I installed 25,000$ worth of kleemann upgrades (will make a thread about this soon). So basically for around 70,000$ total cash spend, I have an SLK that's as fast as SL65 in the straight line and handles a million times better than any SL... couldn't be happier