In my case I didn’t see specific Java problems. The problems that I saw are related to SWT and Eclipse API. WireframeSketcher is an Eclipse RCP app, which means it’s based on the same framework that is used by Eclipse. I imagine that most of the required changes to make strict mode work must be made in the SWT API.
The easiest way to see what changes are needed is to try and make strict mode work for Eclipse itself, and then try and fix the discovered issues in the SWT API. Even if in the end Eclipse will remain in classic mode, the fixes will be useful for other SWT and Eclipse based apps that require strict confinement. I’ve filed an initial bug report in Eclipse’s Bugzilla here: https://bugs.eclipse.org/bugs/show_bug.cgi?id=552387