Mixed Windows / Linux environment

[an3k]

I'm currently in the process of creating a "backup" of my DVD and Blu-ray collection. I use MeGUI on Windows 7 on my already 8 years old Computer (Core2Quad Q9650) and while movies aren't a problem TV Shows like The X-Files or Stargate SG-1 are a huge one, especially Shows on DVD (anamorph, interlaced, overscan). I just added my Notebook (Core i5) as an additional encoder and it's nearly as fast as my computer.

However, I have a very powerful server in the basement (Xeon E5-2680 v3) and want to move all the cpu intensive parts onto that machine. It is running Linux (Ubuntu 14.04.2 Server) thus without a GUI. I can't install Windows, neither as standalone nor as secondary OS because the server is also providing some network services (RADIUS, DNS, DHCP, ...) which have to be running 24/7/365.

I'm sorry for all the following questions but I never used any audio/video stuff on Linux before and I don't know what I need (ALSA? GUI? Graphics Card?) and what problems may occur. Any help is appreciated even if it's just a link without any comment, a comment without any link or whatever constructive

My current workflow for Blu-rays is:

1. AnyDVD HD
2. BDInfo
3. tsMuXeR
4. DGIndexNV
5. MeGUI
   1. AVS Script Creator
   2. x264
6. mkvtoolnix-gui

For DVDs I use AnyDVD HD too but followed by SmartRipper and DGIndex and then MeGUI.

So my main question is: What are good counterparts of the tools used in steps 1, 2 and 4 for Linux? Since txMuXeR, x264 and mkvtoolnix are also available for Linux and I actually do nothing more than cropping (only if the source is not 1,778:1) and converting to YV12 with AviSynth I can use a template here and just edit it with an text editor and thus don't need MeGUI at all. If the Indexer (for Linux) does not automatically crop 1088 to 1080 like DGIndexNV I'll always have to use AviSynth; what is the best for Linux here (AvxSynth, VapourSynth, etc.)?

For DVDs I'd definitely do all steps except encoding on Windows because I'll have to visually create the AVS Script (crop then anti-anamorph) to keep the correct AR. I just hope that QTGMC is also available on Linux.

Thank you very much!