You probably already know that but beginning from 2007, CLS does not have SBC brakes, and not having SBC brakes is a GOOD thing. You don't have to worry about SBC pump failing and stuff.

Plus It is much easier/cheaper to change brake pads and rotors without worrying about SBC system, this may be important if you are planning to keep the car for long term.

Just my 0.02 cents.

 

What are other differences between the two versions. I will also be buying one or the other. Are there any major option differences? Kompressor or Naturally aspirated?

 

The main difference is the engine. And that's a big difference in my opinion. The CLS55 has an AMG 5.5 Liter supercharged intercooled 24-valve V-8 engine with 469 HP and 516 lb-ft of torque. The CLS63 has a 6.3 Liter DOHC 32-Valve normally aspirated V-8 with 507 (38 more) HP and 465 (51 less) lb-ft of torque. I've read some different numbers on 0-60 mph times but one table shows 4.3 sec. for the 55 and 4.1 for the 63. They're both great engines and both got great reviews in the car magazines. I just personally prefer the simplicity of a normally aspirated engine and the sophistication of more valves. Of course all the info I provided here is just statistics. I'd like to hear from someone who has driven both and can attest to their comparative performance and driving experience.

The rest of the drive train is the same - 7-speed transmission. Other than the change in the brakes mentioned in the previous post, I'm not aware of any other differences.

Unless they have extended warranties, I believe they are both out of the standard warranty. The standard warranty is 48 months or 50,000 miles whichever comes first. So the 2006 is out on time (or will be soon) and the 2007 is out on mileage.

 

The rest of the drive train is the same - 7-speed transmission. Other than the change in the brakes mentioned in the previous post, I'm not aware of any other differences.
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I dont' think that statement is correct. Pretty sure the CLS55 has a 5 speed transmission. And the CLS63 has a 7 speed. The higher torque in the 55 was supposedly too much for the 7 speed transmission. Someone correct me if i'm wrong, but that's what i've gathered from what i've read.

Also, you'll see that most people that like to tinker with their engines much prefer to 55 engine. Much easier to tweak a supercharged engine for more power than a NA engine.

I have a CLS63 so maybe i'm partial, but i think it sounds better. (of course that is purely subjective.)

 

If you're looking for additional performance above the stock power levels the 55 is the only real choice.

 

Sorry about the transmission error. dericious is correct. The 2006 CLS55 has the 5-Speed and the 2007 CLS63 has the 7-Speed. I misread the ordering guide I had. These ordering guides are interesting. Below is a link to the 2006 and 2007 CLS Class Ordering Guides:
View attachment Mercedes Benz 2006 CLS Dealer Ordering Guide.pdf
View attachment Mercedes Benz 2007 CLS Dealer Ordering Guide.pdf

The exhaust was also changed in 2007 by using close-coupled catalytic converters which I believe would affect the sound.

Here is a link from WORLDCARFANS.com about the new (at the time) AMG 6.3 engine: New AMG 6.3 Liter V8 Engine - In Detail

The article says: The most important highlights of the new AMG V8 engine:
Cylinder walls in revolutionary TWAS technology
Vertical intake and exhaust ducts
Four-valve technology with two overhead camshafts and bucket tappets
Dual-length variable intake manifold in magnesium technology with two interior throttle flaps
Continuous camshaft adjustment on the intake and exhaust sides
Close-coupled catalytic converters
Oil-water heat exchanger
Solid aluminum crankcase with bedplate and closed-deck design with cast-in steel components

And here's Follow-Up Test Review and Video from edmunds INSIDE LINE on the 2007 CLS63: Follow-Up Test: 2007 Mercedes-Benz CLS63 AMG and a shorter review on the 2006 CLS55 http://www.insideline.com/mercedes-benz/cls-class/2006/2004-paris-2006-mercedes-benz-cls55-amg.html