Hi John,
There is a standard of getting per thread info via JMX, see JSR 174, you might want to discuss this with application team.
Also, CPU timer tracers can help towards this, it measures the CPU time on the thread when the request starts and takes the end cpu time once the request has finished. To measure the CPU time per Thread you will need the thread start point. On most J2EE applications this should be the Servlet service method. Keep in mind that you will get the CPU Time only at finishTrace of a method.
I hope this helps,
Regards,
Sergio