Requirements
• AviSynth with the ffms2.dll plugin and VirtualDub (or some other way to get the frame numbers from MKVs)
• ActivePerl (or some other version of Perl)
• TheFluff's split_aud.pl script
• MKVToolnix (includes mkvmerge, mkvextract, and mkvinfo)
• MP4Box (also available with the Yamb GUI)
• MediaInfo CLI (this is separate from the GUI version)

Notes
• The .avs script must have the same file name as the MKV you want to split from except for the extension.

• Only works with MKVs. It could be expanded to support MP4 and AVI, but almost all current anime is in MKV, other than crappy Xvid in AVI versions.

• Assumes the audio is track 2 in the MKV. This is usually the case, but if it's not, the relevant call to mkvextract needs to be changed to use the correct number.

• Assumes the video frame rate is 24000/1001 (i.e. 23.976 fps). The relevant call to split_aud.pl needs to be changed to use 30000/1001 for 29.970 fps video.

• Doesn't work with variable frame rate videos unless the frame rate doesn't change between the start of the video and the split end point.

• Program paths obviously need to be adjusted to match your install paths. MKVToolnix adds its directory to the Windows PATH and Perl\site\bin is added when installing ActivePerl, however.