Hi,
You can use the "Freeze Transformations" command, found under Modify to zero out the rotations. You might want to check your local rotation axes are also setup properly, and can display them using Display -> Transform Display -> Local Rotation Axes.
If you want to rotate your LRA's, you can do so in component mode. Go to component mode (the blue mode, by hitting F8), and turn everything off. Then right click on your ? icon, to select LRA. Now you can select them and rotate them as normal with the rotation tool.
Your second question about IK rotations: The IK solvers are actually supplying their "answers" as the rotations of these joints. Thus, when you move your IK handle, it rotates all the joints to achieve the end position. This means you can't overwrite the rotation directly.
What people typically do is setup a blend system, with a complete second skeleton for FK, and a complete third skeleton that shows the result. This sounds complicated, but is actually quite straight forward. You create your second and third skeletons, setup your third skeleton to blend between the two. To do so, usually the easiest is to make use of constraints. You could also do the math and write expressions if you prefer. Then you animate on the second skeleton and dial in your blend.
Cheers,
tj