So, I applied the txt files from p.67 which solved some of the problems that I'd been having, namely the error spam when the game decided that caravans were made of chaos and madness, but there's still a good deal of wonkiness in Calradia.
One of the first things that I did after applying the txt files (which was a little annoying since firefox decided that txt files are meant to be displayed, not downloaded and the file host was set up in such a way that I couldn't just right-click/save as. I had to copy/paste everything into notepad. Just a minor annoyance really) was send away one of my companions, to see if they would be able to rejoin me. That met with great success when Alayen came back with a nice long report about a side I was no where near and didn't care about at all. Since the vanishing companions bug was the big killer for me (I usually play with my messages off anyway) I thought my troubles were over. I was wrong.
The Strangeness started innocently enough. It was a slow, creeping thing. Slow enough that I barely noticed it until it reared up its ugly head and struck! At first, it limited itself to minor inconvenience, messages disappearing if several lords decided to try out new toys at the same time. Usually this was after a large campaign and unlike the previous error spam the messages would come back eventually. Sometimes, to lull me into a sense of complacency, the Strangeness was beneficial. My health would be restored far quicker than ordinary men! Even after the most terrible battles it took a mere few steps before I would find myself miraculously restored! My companions were not so lucky, so surely this wasn't the result of my several points in Wound Treatment. My miraculous recoveries were born of the Strangeness but it was beneficial and so I did not seek out its source, much to my later dismay.
As I prepared to embark upon yet another great campaign for the glory of the Imperial State events befell me which would change me forever. The Strangeness reared its monstrous head and like a great beast it roared! The time for my undoing had come! My men and I marched towards the Lion Throne and, not but a few meters from the bridge I beheld my compatriot General von Beseler engaging a band of traitorous deserters in combat. Without thinking, without looking closely at the vileness I was about to engage, I led my men to von Beseler's aid.
The battle was fierce, but short. The deserters were outnumbered, out gunned and out matched. However, even as my men finished gunning down the last of the charging rabble I noticed that one of our foes had remained behind. The coward had stayed frozen in place by fear as his companions had surged forward toward their deaths. The cowardice of this creature dredged up a darkness within me. It was a blight upon the eyes of men everywhere and I would be the one to expunge it. Upon my loyal steed I raced forward, leaving my riflemen behind.
I expected to find a coward, a pale wretch of a man piddling himself in fear and cringing pitifully in the face of righteous judgment. What I found was altogether different. There, sitting confidently atop a great hunter was the Strangeness made manifest. It grinned behind its impressive mustache, a mustache it had stolen, along with every other part of its countenance, from myself! I brought my horse to a halt in front of this terrible blasphemy, this creature which looked upon me with my own face! This was the face of the Strangeness. This was the darkness within me, within all of Calradia. I raised my pistol to its head and with the crack of black powder expunged the vileness from the world.
Or so I thought until I awoke. While I had taken no wounds during all of the fighting I awoke near death after casting down my doppelganger. Ymira, ever my faithful companion, had vanished from my party and no one knew of her whereabouts. Undaunted, I led my men onwards towards the lands of the Lion's Throne. I glanced at von Beseler's party as they passed towards their new destination and fear gripped my belly as I saw that the Strangness guided von Beseler now. The general was leading his men straight towards {!}enemies! I did not know where such a place must lie but surely it was beyond this mortal plane! Surely it was somewhere within the very depths of the Strangness!
Dismayed but undaunted I led my men onwards when Ymira returned! I was ecstatic! It was a worrying thing to march off to battle without one's medic along. As I made to welcome Ymira back however, the Strangeness overtook me! Powerless to resist the awful lie spilling from my lips I watched on as though from somewhere outside myself as I told Ymira that my party was full, that there was no place for her in Godfrey's Rifles. The lie of this was obvious. The Rifles had only fifty men while I had on several occasions led over a hundred! Dismayed and obviously saddened, Ymira left, promising to return again in a few days. I checked my notes to see where she had gone after this disastrous conversation. Ymira's whereabouts were unknown but wherever she was she was happy about Iron Works. The Strangeness had overtaken Calradia.
Cursed be the day that I cast down my dark double, for in doing so I seem to have damned us all.
tl;dr: I think the bug resulting in your avatar appearing with a group of deserters in the source for a few of the other bugs popping up in the mod.