how split a mkv with subtitles

You can use mkvtoolnix, then go to -> output, and -> splitting -> by parts based on timestamps -> and there you can write the beginning and the end of the poart you want extract (without spaces: like 1:02:07-1:04:40, for example).

avidemux too slow

It’s better use (one of) the following codecs for encoding

  • x264
  • libavcodec MPEG-1/MPEG-2
  • libavcodec MPEG-4
  • Xvid 

so Avidemux will be able to optizmize the CPU usage and will be much faster. And the CPU temperature will be lower.
Cfr.here.