Hi ,
I checked from pure c++ project and my project. In the link below I listed warnings that differs in both files. In addition, most of what you pasted here are warnings that indicates assets are successfully saved.
[Diff Log][1]
I think the problem lies here:
MainFrameActions: Cooking (Windows): UE4Editor-Cmd: [2015.10.16-09.25.03:721][ 0]LogLinker:Warning: Can't find file '/Script/TMEditor'
MainFrameActions: Cooking (Windows): UE4Editor-Cmd: [2015.10.16-09.25.03:721][ 0]LogUObjectGlobals:Warning: Failed to load '/Script/TMEditor': Can't find file '/Script/TMEditor'
Probably cooking process can’t handle plugins with Editor module inside if there are classes for custom nodes.
https://dl.dropboxusercontent.com/u/900840/TMTestLogDiff.txt