Krell Duo 300 compared to Evo 302e or 402e?

In my opinion and defining terms (for purposes of comparison only) , your Pass Labs X350 has a very neutral sound.  It is definitely high resolution, but very neutral and very controlled.  Best I can explain it is that the Pass "Class AB" amps have a "very controlled sound" - in that the dynamics seem to be limited or "held in" in some way.  Don't get me wrong - this amp sounds wonderful to a lot of people, but it does not have a lot of slam/dynamics in the mids and midbass.  I would not really call the Pass X350 a "warm" amp.  I think it is rather "neutral".  It's definitely not warm like a Parasound amp would be, or an older NAD amp.  The Pass Labs full Class A "XA" series amps are not really that warm either in my opinion.  They have a thicker midrange, but still pretty good resolution.  However, it's definitely a different sound

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The Krell Evo402e is a conventional "Class AB" amp that is very high resolution and has a lot of dynamics, resolution, attack and excitement.  This is definitely NOT a warm sounding amp.  My friend has one and I have heard it directly.  I would say the Evo is an awsome amp, but due to its very high resolution character, it can easily become out of control if you have something like metal dome tweeters or silver elements in your cabling.  This is where many can say this amp sounds harsh (but it's really not the amp sounding harsh - it's that the amp is very revealing and the synergy with silver is causing the sound to be too fast/bright).  So, you need to pay attention when matching components with this amp.  Stay to pure copper and gold-plated or rhodium-plated connectors for all wiring (speaker cable / interconnects / power cords).  The perceived "harshness" is something you'll have to deal with when choosing any amp that is not "warm".  The Classe "Class AB" amps are another example of this.
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The newer Krell amps (Solo / Duo / Chorus) are all full biased "Class A" (even though they have a sliding bias circuit).  These have the typical very liquidy and smoothed over "Class A" sound, maybe even lush sounding (but not as lush as some other amps).  The liquidy and smooth character of these amps is definitely more forgiving for "harshness in a system" and still has good dynamics and resolution, but the sound is also less "natural" and less "real" with regard to the instruments and vocals.  You would have hear this character to know what I mean.
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In my opinion, the Krell EVO and Classe "Class AB" amps are the most real sounding of the above, but also need careful matching with other components and wiring.

Your Magico S5 have beryllium dome tweeters, which are NOT metal dome. They will be very high resolution, but will not have the harsh breakup of normal metal domes, so I wouldn’t worry about this. As I said, make sure all your cables have gold-plated (or rhodium plated) terminations (spades, plugs, RCA, XLR). The only thing I would really look at is your Nordost power cable. I don’t know the configuration on your Heimdall 2, but Nordost likes to use larger 16awg solid-core conductors and uses silver-plating to increase higher resolution voltage draws. If things are a little harsh with the Krell/Classe, I would look at replacing this cable first.

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The Classe vs Krell is a hard question. They are close. The Classe is very clean sounding and, If I had to nitpick, I -think- the Classe might be more accurate to the input signal. However, I have been somewhat of a Krell fanboy since 2005 when I first got my Krell HTS home theater processor. When I was ready to upgrade, I went through and tried several different processors, but I kept coming back to the Krell and finally just upgraded to Krell S1200U. There’s something about the Krell "discrete Class A" analog and driver stages that just "sing". There’s definitely a "magic" here, in my opinion. The Krell will have a lot of resolution and dynamics, and there will be no lack of "realism" that is common with warm or colored amps. Caphill may have a different opinion, as he owns and loves his Classe amps.

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Few more details. The Classe is fan cooled, so there might be a little fan noise. Classe are 89 lb monoblocks and are smaller which may be easier to move/handle? CT-M600 can be at most 8 years old.
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Krell 402e is very big and heavy at 135lbs. It can be as old as 11 years. If you are looking at power cords, the Krell requires a special C19 IEC 20A connector on the amplifier power cord socket. I recommend the Furutech rhodium variations (FI-32(R) / FI-52(R) / FI-52NCF). I actually have a couple of FI-52 connectors that I plan to put up for sale for $199 each.

Heh, I gues beryllium is metal - I had to google it.  Most metal dome tweeters are made from aluminum or titanium or maybe even magnesium.  These all have rather low frequencies where they flex/resonate and breakup (such as somewhere between 20khz and 22khz.  Sometimes you can raise the resonance frequency as high as 28khz with something like a ceramic coating.  However, these will still be in the range where it will affect brightness/harshness of the natural highs between 10khz and 20khz. 

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The Beryllium tweeter will not resonate or breakup until somewhere in the 44khz to 48khz area, so you really won't hear any breakup/harshness with these.  Diamond tweeters resonate even higher, at somewhere around 75-78khz.