I have a class I (manually) created that's 805KB and has 1,129 methods (as reported by class.getMethods().length). I'll admit that a generator may have started this class since it represents a table with 204 columns, but there is a significant developer effort in the file. It has 507 get*, 354 set* and 129 is* methods. That's 990 right there.
I realize that FindBugs is open source, but for me to change it and change the plug-in I'm using seems like the wrong way to solve the problem. Ideally I'd like preferences/properties to override the 1M/1K limit at the workspace/project level, but if that's too much effort I'd be happy if FindBugs changed it's hard-coded internal limit so my class can be checked.