I may be blowing smoke, but I would assume that you have the following basic sequence. browser -> perl script -> mySql -> perl -> browser.

What you could do is create a java interface that accepts the user input and then passes it to the Perl web form. Then takes the responce from the perl script and returns it to the user. Simply adding another layer to the system. Once you have that you can develop the java to replace each portion of the perl one at a time. The user will only see the one Java front end change so to them the rest will be transparent.

A) browser -> perl script -> mySql -> perl -> browser.
B) Java -> browser -> perl script -> mySql -> perl -> browser -> Java.
C) Java -> Java -> mySql -> perl -> browser -> Java.
D) Java -> Java -> mySql -> Java -> Java.
D) Java -> mySql -> Java.