A hint: if ypou've done all the above but still cannot get the sections to merge do the following:
- select the faces in sections you want to merge
- Faces>Move Bottom (oor Move Top, Bottom is however best if you have other sections that use semi-transparent textures)
- wait a couple of seconds for sections window to refresh.
Then if you have semi-transparent textured sections like muzzle flash that now occlude other faces (if you only used the move bottom on nontransparent faces it must be allright allready) - mark them and use Faces>Move Top.