The most probable cause is valve body noise. 4R's have a tendency not to be the quietest in that sense and tend to get louder with aftermarket vavlebodies like manuals. Of course, noise is more likely when worn parts become impediments - so make sure to use the correct fluid (Mercon V) and to check the fluid with each oil change for level, color, and smell. Other than that it seems to be a common symptom for many, and shouldn't be a huge concern.
- Chris