Is anyone still trying for this?
I have located the actual problems.
First, there is the simple-fix of the global X and Y axis getting scrambled.
The default player faces down the Y+ axis, but rotation is strangely offset by 90 degrees. (X axis acts as Y)
How is this fixed?
1. Just rotate your whole bone cluster model -90 degrees on the Z axis in Object Mode.
2. Do your desired rotation animations in Pose Mode.
3. Then rotate back in Object mode so Blockhead faces at Y+.
If you've done it correctly, you should have rotations working how you want them to, but you might still see problems like bones randomly being offset, which leads me to our second problem.
The player model obviously starts out with some rotation, which is Blockhead's "default" position. Problem is, the process of converting the model to blender, has tripped up all the bones, so blender thinks each of them have x0 y0 z0 rotation, which is not true for some cases like arms being lightly rotated out by default.
It is because of these problems that makes animating nearly impossible, and fixing the second problem is probably something I can't do alone. I'm soon going to stop my work, if I can't soon fix this, because I've already been working for weeks. The new goal here is to find out how to import the bones correctly into blender, if this can be done, then there is a 90% chance everything will work flawlessly. If you read this far, thanks.