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Yes. However I'd suggest extracting them to two different empty folders and seeing what files they change. If they both change the same file... you'd want to see what parts of that file they change and create a combination file. If they change the same bit of the file (e.g. one is citizen_research_rp 2.5 and one is citizen_research_rp 2.4) you'd just have to choose one of the changes to work with. Also note that some parts of a mod may imbalance parts of a different mod... or in the instance of the research fix... they both make take two different methods to make something stronger or weaker therefore creating imbalance (having all the tech levels at level 1.4 AND citizen_research_rp will mean turbo research speed).

If something has event specific events(e.g. mmg I believe?)... and is designed for vanilla yet you wish to incorperate it into a map with more provinces you'd have to expand the number of provinces that the events refer to (e.g. make the HRE events apply to the extra provinces in the HRE). In general though it shouldn't be too hard depending on the mod. Certainly mods atm should be easy to combine.
 
Notepad++ (a free application) provides a very useful feature, by which you can view two files side by side and it will highlight the differences between the two. You can google it.

To compare files, first open two files (open them one by one, and they will both be there as "tabs" near the top of the screen). Click "View" then "Go to Another View". Your two files will now be side by side. Click "Plugins" then
"Compare > Compare". It will highlight any differences between two nearly identical files (one colour for different values, another for entirely different lines). This is invaluable for combining mods.
 
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