Help converting MVC to SBS

[WOODY3d]

I create nice 3D MKV with MakeMkv including the MVC track, it plays great with stereoscopic player, but I need to be able to edit and MKV/MVC is the ONLY format I can't use to edit. I have tried multiple programs convert the MKV to .avi or .mov or .mp4 or .TS or .264 (such as DVDFab and Pazera MKV to AVI) but they always make an SBS that is full of blocky dancing artifacts and is completely unwatchable and unusable.
WHAT TO DO?
I have tried BD3D2MK3D, its useless and doesn't make anything usable, just a bunch of weird DOS garbage files and stuff that never opens correctly. ( I run the .cmd and it makes what I assume is an SBS .264 file, but it is corrupt and never opens, tried multiple times. Useless.)

I have tried tsMuxer but cant figure it out after weeks of trying (and there is no real info out there except to say the damn thing 'Muxes and deMuxes' (gee that's helpful...)

Can someone tell me why the SBS turns out BLOCKY and UNUSABLE or suggest a tool that actually works? I just need to do it with one disc for work purposes.

THANK YOU!

[Cornucopia]

Mkv2avi and then edit, then stackhorizontal and resize down to sbs. But understand you are losing a few generations and the final codec isn't as efficient, so you must adjust accordingly.

Scott