If I wanted to copy script over from one mod to another, as a sort of merge of the two, would I use TES4Edit to do this or do I need to do this manually with the CS? If the TES4Edit route is possible, how would I go about doing this? About the only thing I've done with TES4Edit is clean files.

I would just do it manually - with the CSE it's as easy as a right-click copy.