Mr.Bones truebones.com has also released a free conversion of the CMU files, which I've found useful.

I don't think messing with your figure's scaling willl help.

I use lots of bvh files, but accept that they are likely to need considerable work, even the best mocaps will need some adjustments to suit the character. They are based on "average" people and take no account of superhero chests or amazon brassieres.

Editing the .bvh in wordpad or similar to make sure as many of the body part names match your figures hierarchy can help. After that it's down to the slog of dragging keyframes around in the graphs.

Keep a T-pose at frame 1 as a referrence to your figure's "normal" settings and the look through the graphs to see where the worst distortions appear, start with the hip and work outwards. Any spikes in the graph will show the first frames that need sorting.

Common problems like arms poking into the body can often be fixed with a blanket adjustment to the collars.

As a rule I delete any side to side keys for forearms and shins and force limits on bends to eliminate all backward bending, to my mind these are false data created by misinterpretation of shoulder or thigh twists. The flat rows of keys are then a guide to the sectors that need fixing in the joint above.