how do I change the starting position of a clan using PFM or DAVE, especially if it concerns a faction which is not contained in the main game, but got added through the Morning Sun-Mod?
Unfortunately, we can't modify mods in the official tools. Its impossible. You can however change a modified mod's start_pos from the ESF window in PFM!
Read husserlTW's introduction to start_pos modding, find the change region ownership tutorial, read very carefully and do your best, and ask if you have questions. I already know, these are Empire tutorials you say; so when you get to the part where he asks you to find two integers in lines 14 and 15, you'll actually find those integers around lines 18 or 19 for Shogun 2. Don't be intimidated, just please read the steps very carefully, you may even want to grab a pen and paper, but you will be fine. There is another way. It requires you to download a library of jruby kernels, do some dos commands, wait a lot, and Notepad++. If you're only changing one region's owner, I recommend the former. If you are changing many regions, you will definitely want the later.
Shogun 2 Mods:
Spoiler Alert, click show to read: