I'm basing this on 3 facts:
1. In 2015 it's highly unlikely that you could build a home-made clock that would be of the size and shape resembling a bomb - that is, unless it was made to look like a bomb.
2. Ahmed, his father, and anyone else with a phone camera (that is on Ahmed's side) would have posted a picture of the clock, or given a full description of it (size, shape, etc), in defense of Ahmed - that is, if it made sense, otherwise they would not. And I have not been able to find an image, nor a good description.
3. The initial teacher told him not to show it to anyone. You can break this down into that teacher having one of two opinions: A) It really did look like a bomb or B) its all about racism / hate / being anti-Muslim / anti-brown in that school (check the school's panel http://www.irvingisd.net/domain/2031 - that school is half brown and black).