How can I help my 5th grader prepare for Junior High?

I agree with the other comments on taking your son on a tour of the school as arranged through the school.  Familiarize yourself (and have your son) with the school, where key areas, like the library, main office, gym, student cafeteria are.  The more you both become familiar, the easier the transition will be.  As a parent, I encourage you to not only talk to the principal, but to other teachers and other parents.   You can also take him informally after school just to walk through the campus. 

Another recommendation is to be sure your son has developed good study skills, time management and organization skills.  These study skills include developing strong reading abilities to be able to comprehend anything he reads and being able to effectively highlight key notes in his books (not highlighting the entire books but key passages/aspects).  Strong time management and organization skills include regularly using a planner now to list homework assignments with due dates and other assignments and keeping a fairly organized backpack with the basic tools for learning (paper, pencils, pens, erasers, highlighters, etc.)

You mentioned that your son is sensitive, so you may want to check with the parents of his friends to see if they are going to the same school as your son.  If they are, that should help make the transition easier.  Your son and friends will likely stay together on the first days of school, and hopefully your son will develop new friendships once he begins to feel comfortable.

You may also want to check with the Jr. High principal to see if the bell schedule for 6th graders is different from the other grades.  Most/all the public schools in my state (California) have separate nutrition and lunch periods from the older students (7th and 8th).  This allows 6th graders to share these periods with 6th graders only, thus helping to ease that transition into a larger schools with multiple teachers and classes.