To be more specific, the .xlsm files have absolutely 0 effect if they're there when the mod is loaded into the game. So their presence shouldn't be messing anything up by themselves.
Your SkillSet.txt can (and should) look something like this:
new skillset "Henchman_Jahan"
add skill "Rain_Water"
add skill "Projectile_BlitzBoltStart"
add skill "Target_ChillyWind"
add skill "Heal_RegenerateStart"
add skill "Teleportation_FreeFall"
add skill "Target_InstantPressure"
add skill "Projectile_StaffOfJahan"
new skillset "Henchman_Madoc"
add skill "Target_StunStart"
add skill "Rush_RushStart"
add skill "Shout_WhirlwindStart"
add skill "Shout_MeleePowerStance"
add skill "Target_HelpingHand"
add skill "Projectile_StaffOfMagus"
The skills that are added can be modified. The names of the skills that are added to the Henchman come from the game's own SkillData.txt (and your mod's SkillData.txt, if your mod has one). What does your SkillSet.txt look like for those two skillsets?
The Character.txt file has no bearing on the henchmen's equipment. Their equipment is defined in the Equipment.txt in the Stats/Generated/ folder. By default, their equipmentset looks like this:
new equipment "Henchman_Madoc_Paladin"
add equipmentgroup
add equipment entry "WPN_DecorationSword_Henchman_Madoc"
add equipmentgroup
add equipment entry "ARM_Leather_Torso_Henchman_Madoc"
add equipmentgroup
add equipment entry "ARM_Cloth_Boots_Henchman_Madoc"
add equipmentgroup
add equipment entry "POTION_Minor_Healing_Potion"
add equipmentgroup
add equipment entry "POTION_Minor_Healing_Potion"
add equipmentgroup
add equipment entry "ARM_Cloth_Bracers_Henchman_Madoc"
add equipmentgroup
add equipment entry "ARM_Garment_Sourcehunter"
new equipment "Henchman_Jahan_Mage"
add equipmentgroup
add equipment entry "WPN_Quarterstaff_Henchman_Jahan"
add equipmentgroup
add equipment entry "ARM_Cloth_Torso_Henchman_Jahan"
add equipmentgroup
add equipment entry "ARM_Cloth_Boots_Henchman_Jahan"
add equipmentgroup
add equipment entry "POTION_Minor_Healing_Potion"
add equipmentgroup
add equipment entry "SCROLL_Resurrect_1"
add equipmentgroup
add equipment entry "ARM_Cloth_Bracers_Henchman_Jahan"
Note how there are no spaces, and how the 'start' lines for their Equipment entries are the __ new equipment "Henchman_Madoc_Paladin" __ and __ new equipment "Henchman_Jahan_Mage" __ lines. If you want to add new equipment to them, presumably your Equipment.txt file would have to follow a similiar pattern.
Edit:
The Character.txt does affect their stats though, so depending on how you want them to be built/start out that's worthwhile to change. What do your Character.txt entries for them look like?
Edit #2:
Oh right, this is something I don't think is well known, but the Character.txt *does not* import any data from the Main campaign's Character.txt file. So if your Jahan entry looks like this:
new entry "Henchman_Jahan_Mage"
type "Character"
using "_Hero"
data "Act part" "3"
data "Strength" "4"
data "Dexterity" "4"
data "Intelligence" "7"
data "Constitution" "6"
data "Speed" "4"
data "Perception" "5"
data "Gain" "None"
data "Willpower" "1"
data "WaterSpecialist" "2"
data "AirSpecialist" "2"
data "Talents" "Scientist;ElementalAffinity;FaroutDude"
Then it won't work unless "_Hero" is defined in the *same* Character.txt file somewhere above the Jahan entry.
