I have a 5 speed d15b7, the noise is a random growling noise, I repaced the engine for other reasons and it is still making the noise. It is very random, it only does it when accelerating, and doesn't do it all the time, It does it in every gear also.
I am thinking it is some sensor or something.

 

is it the tranny? A bearing could be the problem!

 

I just put the new engine in yesterday, and the TO bearing was replaced, if thats what you meant by bearing

 

What about the pilot bearing? Hate to say it but might be something internal, however if you swapped a motor you could crack it open in to time.