This is a difficult one to answer depending on your definition of transsexual. Usually this refers to people that have undergone some sort of sex change operation.
Tijuana has a very large homosexual and transgender underground population and community, but it's relatively isolated from the rest of society. If you're simply looking for men that dress like women and possibly inject hormones etc., then there is an area near the zona norte where the police tolerate the transgender people to stand out on the sidewalk. You'll find this area near 2nd street and west of Martinez. I'm sure if you pulled up and asked one where to go, they would know.
There is another place called Africa, (least it was years ago) that is near Blvd Cucapah that did have some transgender people as well as regular women working there. It's a gigantic place with a vaulted cathedral ceiling, but concrete for the floor. Strange place indeed, but they might have what you're looking for as well.
As I said above, I can't comment on who has undergone a sex-change operation because I don't really follow that scene. I have some employees that I assume are tied in with that crowd, but it would be against company policy for me to ask them questions about their private life.
Look for the place called Africa, and there's another place on the same boulevard and I swear for the life of me I can't remember the name, but I heard there were some transgender people there as well. Take Blvd. Insurgentes and take a left at the intersection of Wal-Mart and Calimax where the buses stop. Follow the road up, take a right next to the materials factory and then it will dump on to the main Blvd. Cucapah. There's about 6 or 7 strip joints and night-time places on that boulevard. If that fails, then go 2 blocks west of Martinez in Zona Norte and ask the peope on the sidewalk and they should know as well.