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In case you haven't figured this out yet...
When you add your .bip file you should scale the biped to better match your character, it's too tall as it is on the screenshot, this is located in the info window when you select add motion capture file from the layer manager of the CAT roll-outs, you know where it is because you made it to the mapping window.
You may need to adjust this a few times to get it right by just adding the motion file again, adjusting the biped height down more, then delete the other wrong scaled biped, by selecting any bone on the old one and hit delete key, easiest way. (careful not to delete the wrong biped).
If any bones come in 180 rotated, they may or may not, but don't worry it happens, just carry on and fix it after you capture the motion to your CAT rig character.
I see in the screenshot the mapping is still red, means you didn't click the button for source object and hit auto-map, then click the button for Base Human 001, (or whatever you named your CAT rig), and hit auto-map again, red line will disappear, or should now, and rig should be properly mapped.
Then click Capture, when it's finished delete the source when prompted, your animation should be baked to your CAT character now.
Then, if arms are still rotated wrong, go to first frame (0) and rotate them correctly, they should now maintain this rotation to match the animation, you can do that with any bone rotations you feel are off.
There is an issue that may happen with the feet, and probably will, where you have to go into the limb animation roll-out, select the IK for the foot in the scene and click (select limb end), then rotate it to be flat with the floor and IK controller, if this puts the rig off the floor, as it will, click the 4-green arrows (layer transform gizmo) in the layer manager section, click on the root node in the scene, (box between the feet), and select move tool and position it correctly, then untick the layer gizmo.
Your animation should then work fine, if not, you need to try again, until you get the process down, it will take a few attempts, just how it is, I know it should be easier, but I haven't found a way yet, you will get more familiar with it as you do it more.
You can also just add the BVH file the same way, but it will bring in a stick figure instead of a biped, do scale the same way, but works in a bit different way for adjusting things, a bit more involved, so using a BIP file is probably better.
Hope this helps.
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