In your hypergraph, pelvis should at the top of the hierarchy.

To make the pelvis joint more easy to select, I will select the pelvis joint and -> Display -> object component -> Selection Handles to display it¡¦s selection handle. Then, toggle to Select by Component mode, select +.

Then select pelvis's selection handle from pelvis joint, moves it away from the pelvis joint. When this done, we will be able to select pelvis joint easily.

Reorienting Local Axes of Joints

To show joint's local rotate axes, select the joint, go to Display -> object components -> Local Rotation Axes

As you can see from the bone I've created with local rotation axes shown, Y-axis is pointing down the bone, This is what we want. But after we translate the joint to fit it into our model, Y axis will no longer pointing down the bone anymore, and this will mess up the joint's rotation, this is what we don't want.

So, we need to reorient the Y-axis. To do this, we need a MEL command to help us auto reorient the Y-axis. Key this joint -e -oj yxz -zso -ch; in command window, you can edit yxz to xyz to suit your need. First alphabet is the axis that pointing down the bone. You may like to save this command in your shelf by MMB drag the script from command window to shelf .

We will use another Mel command select -hi; to help us to select all joints in hierarchy. Save these commands into your shelf, it's very useful.

1. Pick the pelvis joint and apply select -hi; to select all joints in hierarchy.
Go to Display -> object components -> Local Rotation Axes to show all joints' rotation axes.

2. While the bone still selected, I applied joint -e -oj yxz -zso -ch; to reorient the joints.
Check the joints reorientation carefully, if everything ok switch off display local rotation axes.
Now, I have our bones ready. Next, I will proceed to IK setup.