If you used JSGME to put the files into your mix, just use JSGME to remove them. A few questions for you on the missions' use:
1. Which version of SH4 do you have? ie: 1.3, 1.4 or 1.5
2. What other mods do you already have activated?
The symptoms you describe are similar to what you encounter when either the mod isn't compatible with your version of the game, or with other mods you have activated. If I am not mistaken, those missions are for use with
Nisgeis' 3D TDC and Radar mod on the Stock game, using
JCC's TDC tutorial vid, of which there is an older thread somewhere on SubSim here about all that... I had it all bookmarked on my usual computer, but this is a borrowed machine I am on now...