Hello,
Here is a freeware tool that I found. It can compare 3 files at the same time and merge any changes from any of the 2 to the 3rd one.
The program has 3 panes. The idea is to open the original file from the SH folder in the middle pane and the 2 mods that you want to merge on the sides.
By reviewing the differences (the app jumps automatically to the next line that is different than any of the others) you are able to compile a new file that has all the functionality of the original plus the combined changes of the 2 mods that you want to merge.
Merging modes is easier than ever. No more conflicting mods.
Link for download:
http://www.sourcegear.com/diffmerge/downloads.html
Another tool to the disposal of moders. I hope it will be useful to someone.