I tried modifying the standard Henchmen (bard, torchbearer, and shieldman), however when you go to chose the traits the Henchman traits are not there and dont show up so they can be selected.

I ran into the same problem with the henchwomen that I modded in.

For your henchmen did you edit the unit files? Namely does this line exist in your unit definitions for these henchmen

          <UnitModelType>HenchmanMale</UnitModelType>

This is important to unlock all the special abilities and items.

Otherwise you are going to have to do what I did with the henchmanfemale and go through EVERY single item that you want that model to equip.

check out my mod to see what I mean.