FactoryFinder performance/bad caching

35 ms sounds like there is disc access times involved, and that points to a problem with OS cacheing.

If there any directory/non-jar entries on the classpath that can slow things down. Also if the resource isn't present at the first location that is checked.

ClassLoader.getResource can be overridden if you can set the thread context class loader, either through configuration (I haven't touched tomcat for years) or just Thread.setContextClassLoader.