It's possible that Howard played some of the wha-wha in the score for the movie, but may have copied what Skip did for Isaac Hayes on the original...
Just guessing here, obviously, but there are a lot of cut scenes and incidental music in the movie that use the motif...
The CNN interview pretty much nails it for me (link on the Wiki Pitts page), but, as with most things film score orientated, there are probably a lot of details we'll never know...!
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