I think I know the problem with the new clothes disappearing when you take them off:
Are there any files of the clothes found throughout the game? Maybe you should make new files of the clothes you made yourself...
PS:
The files for the clothes are probably those examples listed here:
wear_scientist.SMF
wear_aofficer.SMF
Maybe you can make files like:
wear_professor.SMF
wear_colonel.SMF
wear_scientist2.SMF
And hopefully they'll solve the problem with the new clothes...