I´ve figured out how to use the shift animation tool now, not entirely intuitive so here is a little tutorial:
By default ALL frames are selected, haven´t found a better way but if you just click "go" and then ctrl+Z to undo, you can now select to move only inside one frame.
By default the body part you´ve selected is what you´ll move. Haven´t found a way to move all parts of a body yet.
You set the direction you want to shift with LEFT CLICK, opposite of the GUIDE LINE
The guide line is by default up in the left corner, this prevents adjustments in half the directions so use RIGHT click to move the guideline anywhere (a red cross hair shows up to show its location).
[Suggestion: To make this tool more intuitive, having the guideline show up centred in each frame by default would help, with a check-box to hide it]
The LEFT CLICK and pixel movement is then RELATIVE to the red cross hair guideline.
Example: Right click on the SHIFT ANIMATION frame you´ve picked. This sets the red GUIDE LINE.
Now LEFT CLICK one pixel ABOVE the red cross hairs and click GO. The body part will move DOWN 1 pixel. If its the first time, ALL of the selected frames will move if you click GO! (i.e the same as if you clicked GO FOR ALL FRAMES, the second go button). CTRL+Z to undo and now do it again to just move 1 frame at a time.
Left click diagonally UP to the RIGHT, and the body part will move diagonally DOWN-LEFT.
Basically it works like a joystick in an aircraft (inverted input). [Suggestion: An option to have it not inverted could also help.]
There´s probably more commands here that I´ve not figured out yet, but this tool is fantastic for adjusting misaligned arms and such in movement cycles or finding over-flowing pixels that stick out and show up in other frames.