Try using Portecle to import all your stuff. I haven't used it myself, but the complete mess that is Java Keystores is evidently a lot more manageable if you use a tool like Portecle.
If you want to get better performance out of Tomcat and not bother merging your keys, certs, etc. into a single binary ball, consider using Tomcat's APR connector. You can use the same cert and key files you already use with Apache httpd, and you'll get better crypto performance.