As an Egyptian I was in the US from 1997 to 2002 as a research scholar on the F-1 visa (to do my PhD) and took advantage of the tax treaty with Egypt.
I am now German, and work in the US as a researcher since one month (for the public sector) under a J-1 visa. Can I take advantage of the US-Germany tax treaty for the first two years of this stay in the US ?

As per publication 519. U.S. Tax Guide for Aliens, page 6, col. 3; Teachers or Trainee.
"You are not an exempt individual as a teacher or trainee if you were exempt as a teacher, trainee or student for any part of 2 years of the 6 proceeding calender year."
Thus on J-1 you are exempt from residency.

You are also resident of Egypt before coming to the U.S.
You should be able to get the treaty benefit on J-1.
Still you should get comments from AtlantaTaxExpert [email protected]