You can already verify if the THD track has been demuxed. It should have the .thd or .ac3+thd extension. And it should be referenced in __MUX_3D_options.txt.
Yes, using 64-bit x264 is a bit faster (especially with slow presets). Note that avisynth is a 32-bit program, and therefore it cannot communicate directly with x264 64-bit. It's why its output is read by avs2yuv.exe (32-bit), and then piped to x264 (64-bit). There is a very little overhead due to avs2yuv, but anyway the speed gain is still interesting. Don't expect a major gain, though.
Thanks for your appreciation of BD3D2MK3D! :-)
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