Someone else had that same problem of their mod only spawning the last structure added to WorldGenCustomStructures, and I remembered that the solution I found was what a commentor named Redstone Tim mentioned, that in WorldGenStructure you have to remove 'static'. I'm happy to email my version of these two classes to you if you want to have a look. It took me hours and hours to get them working. I have no idea what might cause the cascading gen lag, but fixing the multiple structure problem might help.
[1.12.2] Multiple Structure Generation
in Modder Support
Posted
How did you fix it? Thanks