Does aligning the antennas increase the power of the system?

The antenna are not of a focused directional design. They radiate the energy in practically all directions from the transmitter. The tuning adjustment point is almost the same, until you put the coils into the path. Then the power levels can be affected because then the coils are part of the field. They will interact, and disrupt the scalar field.

It is always best to keep the coils behind the two antenna creating the field. Apart from that, the lids do not need to be perfectly aligned.

You can increase field strength by separating the boxes with more distance.

For more details, please check the link:
https://www.spooky2.com/forums/viewtopic.php?f=117&t=9809