I found my old questions and some notes about lighthouses to perfectly fit to terrain. It is in this thread:
http://www.subsim.com/radioroom/show...=206346&page=2
And some note about lighthouse table:
http://www.subsim.com/radioroom/show...&postcount=172
There is written, that SH coordinates are modified to fit SH map, and real coordinates are real coordinates of real lighthouses. But remember, that when i'm talking about SH3 world, i mean GWX map (there are some modifications - Kiel canal for example, which in vanila SH3 are not... )