Their is a much better way then Hand combining out their, I use a combination of CustomEventManager for Python triggered Events and ModSwitcher for XML additions and alterations.
ModSwitcher is still in its early stages and isn't perfect (i've found a few things it failed to combine properly) but it will achive the equivilent of hours of cut and pasting for you in an instant. As long as no two Mods attempt to add the same element twice or try to alter the same existing element, then it will work. If their is a collision it tells you ware it is.
CustomEventManager was originaly created over at Poly and I created a fully extended version that you can plug python moduels into (assuming the author wrote it well and didn't just insert their code in EventManager). From their I can activate or deactivate any Python Mods by comenting out the call.
To make Merge files with ModSwitcher I cleanup the original mod by striping down to the bone everything thats duplicated content. All the XML files will contain only the Element/s the mod adds or alters along with any new files it adds such as artwork or python scripts. Modswitcher sees turns that into a nice efficient Mergefile of only a few K. I try to make it as modular as possible so for example when I borrowed some buildings from the Mylon Mod I broke them up into seperate files and can select at compile time which ones to include.
Their might ofcorse be some dependency issues, if one Mod references new material added by a second mod then you will get XML errors when Civ launches if you left out something at compile time. This shouldn't be too hard to avoid if people know what their doing.
When Modswitcher compiles my chossen Mods it drops the contents directly into my CustomAssets directory. If I am only using XML based mods or game Interface mods then I am ready to play right now. But if I have included any Python Events then I also need to copy a CvCustomEventManager with the apropriate calls and imports into CustomAssets as well. I just keep a master backup copy of this and add in new calls and imports when I find a new Mod. Ofcorse you need to make shure that your not importing and calling any Mods that you didn't compile with so check to make shure comenting matches your compilation choices.
ModSwitcher can be found at:
http://forums.civfanatics.com/showthread.php?t=140188
And my CustomEventManager at:
http://forums.civfanatics.com/showthread.php?p=3474468#post3474468