, I'm totally loving this thread and I'm sitting here at my computer smiling as I read your progress reports. There's catharsis in this thread. And I'm impressed not only with your willingness to tear the car apart but your rather articulate way with which you describe the goings-on. That you're kind of OCD about your car is even more delicious, and that someone gifted you a complete replacement parts car is just over-the-top good.
I like my cars to run exactly as they're designed, and I'm very attuned to what the car is supposed to sound like vs the presence of strange noises, rattles, clunks and what-not drive me crazy. I spend more money and time than I "should" in ferreting out anomalies; it's my version of car OCD. For example, currently, there's an überannoying rattle emanating from what sounds like just the roof attachment behind the back seats—obviously only when the roof is up—and it's driving me nuts because I don't have convenient access to someone to sit in the back seat and narrow down where it's coming from while I drive. And my ventilator fan bearings are on the way out as I have a chirping bird at low-medium fan speed. Oh, and my roof won't lift on its own; it needs a little helping hand when the hydraulics are attempting to lift the front—hopefully just a cable adjustment.
Anyway, last year August I bought an '03 CLK430 with only 69K miles on it in what was rather amazing shape. I was very excited about it as I'd always wanted a convertible. I wasn't looking for a V8, but I'd heard the M113 engine/723 transmission combo is strong and long-lasting when cared for. I initially was a bit worried about gas mileage (like you, I also have a Honda, though mine's an '06 Civic si and not the S2000), but the 113 engine actually averages 20 combined city/highway—quite respectable for the early 2000s. But it had second-rate tires on it (Benzes just go gaga for Michelins and Pirellis), and, like your CLK, I knew it would need front lower ball joints as the play was noticeable on the rack. Also, one of the motor mounts had collapsed, so I knew I'd be in it for those. The ventilation fan didn't know whether to scratch its watch or wind its butt, so I suspected the motor regulator was shot. And the ride was a bit floaty/sloppy—so i suspected shocks. I was surprised that I'd need them at 69K miles, but it's not exactly a featherweight car. But the saying goes, "There's nothing quite as expensive as a cheap Mercedes-Benz."
So after spending a few grand comprised of ball joints, motor/transmission mounts, fan regulator, cabin air filter, replacement (Bilstein) OEM-spec'd shocks, Michelin Pilot Super Sports, transmission and oil service, and a stereo replacement (I took out the OE radio and CD changer in favor of Bluetooth and iPod integration—I made a choice to live with "Pioneer" on my radio instead of "Mercedes-Benz"), I'm happy as a clam at high tide. This car runs SO well. I just drove it 1,400 miles up and back from San Diego to SF and then down Highway 1, and it's just a lovely road car. Sure-footed (slight understeer but it's OK) and agile and a lot of fun to drive.
I'll from time to time check in on your progress. These cars are old enough now that while there are still a fair number on the road, but many of them have faced some neglect. So when I see one that's been cared for or has been given a lot of TLC and facelift, I get kind of excited. Good luck with your project!