you must remember that the computer audio DSD playback is in its very early infancy, and that a lot of this stuff is bleeding edge. Furthermore, there are no definite answers to some questions, as we are all learning more and more.
1) Yes, the current sacd-extract.exe creates a slightly audible click at the begining of each extracted DSD track that is not gapless (i.e 4 seconds or so of silence). Mr Wicked and friends are diligently working to fix this. Some players and some DAC firmware make it less obvious (for example, in Mytek firmware 1.3.3 and PM 1.84 the clicks aren't obvious at all, but the Mytek input PLL timers for PCM-to-DSD switching aren't exactly timed perfectly yet (a Sabre chip issue) so you might get a couple notes at the beginning of the next DSD song sound like it fades in. Simple fix is to restart song, or revert back to fw 1.3.2....yadayada. it will all be rectified soon, but this is software folks..
2) Worth buying?? Only you can decide. Us Mytek DSD listeners have all types of computers, ranging from my 2009 Mac Mini with Hynes ps, to DIY Linux boxes to Windows boxes. My Mac Mini is not tweaked by Mach2 but they do good work.
3) Mytek has been in business for a long time. "Infant diseases" here are mainly DSD-to-the-consumer in nature more than anything. The brand new clever-but-unique dCS DSD-over USB (and firewire) protocol is barely out of dCS's programmers hands, the USB drivers are all very different, etc. Specific to Mytek, the USB drivers work fine for Windows, and the Firewire ones work for both Windows and MAC. I can't speak for Linux (firewire) but it sounds like its good from all reports here. As stated above Mytek and it's partners (ESS Sabre, Rigisystems,. Dice,e tc) are all working together to get all this right. in the meantime us listeners are dealing with minor hiccups and major musical nirvana. The DAC itself, like most any, requires a good 300+ hours to uncover its full potential.
4)I like the Granite digital fw cables, but others like Belden and Oyaide, which is the most expensive but only tips the scale at $100. I like Mytek's XLR outputs and use Furutech Evolution II Ref 3's. Since you describe your amp as warm, the more neutrla (like mine) will likley work best anyway.
5) Most people who have had Mytek high voltage output issues has to do with preamp input sensitivity, not power amps per se. Dunno though; others need to chime in. I would doubt this is a deal breaker.