Since finding out about this issue I've changed from Version.dll to Online content unlocker and scripthooks dinput8 file and completely removed Whyem's and my stream, I've got a good 4-5GB of mods such as Munitions, hunting grounds, Needs, thirsty horse etc and since removing the stupid amount of YTD's I had in my stream folder and WhyEms (I removed Collyrium too, though IDK if it had any effect, did it just to be safe.) and in a 40 minute playthrough i've already came across 2 passenger trains and 2 supply trains out in free-roam, the passenger trains each have 4-5 passengers each carriage with the normal amount of guards. Birds spawn rate is immediately higher, haven't been able to test the beggers yet as I'm in chapter 3 and had to ignore the life out of them previously do not sure if they'll spawn again but everything else seems to be working great.
Looks like the culprit was the YTD files for me.
