Sorry for the late reply. The lights just about fit in the 2x4, the blocks are just set up between the lights so everything looks even. I don't measure the distances between them, just by eye.
As for the distance I have the lights above the canopy, I start of at approximately 50cm. The lights are on full blast, 24/7 they only draw 220w from the board so are cheap to run. Having the lights on like this also helps keep the environment stable.
Once the plants are framed up I lower the lights to about 40cm, I've never used a light meter, it's all just done by feel.
Don't worry about short thick stems, the thicker stems will be able to carry more nutrients a shorter distance. Short stems for this method are actually desirable