The Punisher

Haven't looked at the model but seems you don't have any head tags (*head_front, *head_back, *head_right, *head_left, *head_top, *head_eyes). Maybe when you  swapped the head you forgot to re-parent the tags and when  exported the model, they went missing.

Without looking at the model would be difficult to identify the actual issue but the issue on the screenshots seems to be a naming issue. Seems you have 2 "meshes" with the same object name (in the ghoul2 properties), therefore one of them is over-written by the other during export.
 
As for the seams issue, there are a few posts about it. You can check https://jkhub.org/topic/8009-assistance-needed-for-blender/?hl=%2Bseams+%2Bfrom+%2Ban+%2Bisland&do=findComment&comment=115635

Open the pk3 in packscape
go to modles\players\kylo_ren
copy model_default_tlj.skin file to your hardrive and open it
change the line
torso_cape_tlj,models/players/kylo_ren/cape.tga to
torso_cape_tlj,*off Save it as model_default_tlj2.skin
 
move it to the modles\players\kylo_ren inside packscape
 
go to ext_data\npcs
extract kylo_ren,npc to your hard drive and open it
copy the entire "Kylo_Ren" NPC section and past it below
rename the new NPC to Kylo_Ren_TLJ
add the line
 customskin     default_tlj2Save it and move it back to its place inside packscape
Save the file in packscape
 
use
 
playermodel kylo_ren_tlj

It means you haven't property setup you working folder structure and Blender can't find the default skeleton file in the _humanoid folder.
 
Check this:
https://jkhub.org/topic/10172-blender-jka-frankenstein-modelling/

Sabers usually have the texture names hard-coded into the ".glm" file. In this case, it points to "saber_ventress" but the folder name is "saber_ventressk" 
 
 
 

https://jkhub.org/topic/6236-the-path-of-the-apprentice/page-32?do=findComment&comment=135203

Try a 3rd party uninstaller, like ZSoft Uninstaller, Smarty Uninstaller, Should I Remove It, Wise Program Uninstaller or Revo uninstaller (there is a 30 days free demo).

Shouldn't be an issue. The path is followed by dots. Just overwrite the dots. In the screenshot below, I renamed the Clone Wars animations to "_humanoid_cwv6" so i could use it with specific models. As you can see in both, the number of characters and the file size remained unchanged....
 
 
 

Going back to your problem, you should be good with OpenJK. I can use most models without any issues (as long as the model has 10K verts or less, if it has more, even with OpenJK you will have the same error).