Ok, let's begin
Decoding software - JM Reference Software with my modifications
Tools needed:
1. Transport Stream Packet Editor (v0.81) (for demuxing raw 264 streams)
2. eac3 (optional) for sound extraction
3. YUVTools_3.0 (optional) for checking output yuv file
4. ffmpeg  for reencoding right stream
5. MKVtoolnix/mkvmerge.exe for muxing into mkv

Warning: JM produce very large raw yuv output files (f.e-1m:13s -> 10gb (5 for left & 5 for right)

BD structure:
00004.ssif=00004.m2ts+00005.m2ts
00006.ssif=00006.m2ts+00007.m2ts
00008.ssif=00008.m2ts+00009.m2ts

For example, we will use 00008.ssif (schreck)

1. Preparing raw streams. Run TSPE, open 00008.m2ts (left eye stream), uncheck all streams in tree except 0x1011 [tree - pat pid+0x100+0x1011]
2. Set output directory
3. Set options -Demux - Demux raw streams
4. Click edit
5. Rename output file 00008.Demux.1011.264 to left.h264
6. Reopen program, open 00009.m2ts, uncheck 0x1011, check 0x1012
7. Set output directory & options -Demux - Demux raw streams
8. Click edit. When message 'No elementary stream PIDs selected for demuxing' appears open tab 'PID Line'. Click edit again. Ignore message 'Warning: source contains no video PID.'
9. Rename '00009.Demux.1012.es' to right.h264
10. Download modified version of JM http://www.multiupload.com/XPEQEJENAQ
11. Unpack it
12. Working directory should consists of decoder.cfg,ldecod.exe,left.h264,right.h264
13. Run ldecod.exe and wait some time
14. Output files:
test_dec_ViewId0000.yuv (left view)
test_dec_ViewId0001.yuv (right view)
Left view:
You can use left.h264 or re-encode test_dec_ViewId0000.yuv
Right view:
You must re-encode test_dec_ViewId0001.yuv to h264 stream
For example, we will use ffmpeg.exe
Run 'ffmpeg.exe -s hd1080 -i test_dec_ViewId0001.yuv  -vcodec libx264 -b 4560000 -bt 4560000 right_f.h264'

--
Sound extracting
Run eac3to.exe 00008.m2ts 3:sound.ac3

Ok, final part, muxing
1.Run mmg.exe (MKVtoolnix), click add, left.h264, set format specific options - fps - 24000/1001
2. add sound.ac3
3. Click 'start muxing'. Final left file - left.mkv
Right file
1.Run mmg.exe (MKVtoolnix), click add, right_f.h264, set format specific options - fps - 24000/1001
2. Click 'start muxing'. Final right file - right_f.mkv

That's all folks wink