I don't know much about zipping and uploading files, or about using the type of installer that could automatically overwrite the needed files, but all you need is really already on your computer.
Go to C:\Program Files\Firaxis Games\Sid Meier's Civilization 4\Beyond the Sword\Mods\Fall from Heaven 2 025\Assets\XML\Gameinfo, then replace the CIV4EspianageMission.xml with the file of the same name found in C:\Program Files\Firaxis Games\Sid Meier's Civilization 4\Beyond the Sword\Assets\XML\GameInfo. This is the normal BtS file, it should be about 30 KB as oppesed to the mod's version which is about 3KB. Actually, now that I think of, I believe the game will look here anyway if it doesn't find the file in the mod's folder. Therefore, you could probably just delete FfH's version instead.
Once this is done, you can do all the espionage you want, if you have the espionage points. Of course, there isn't a way to get the points yet (except through a few rare random events that were unchanged from vanilla BtS). To fix this, you need to make some buildings or specialist provide the points. You could copy the BtS version of CIV4SpecialistInfos.xml over the normal one if you want to allow the new spy, great spy, and great general specialists (note that you need to either edit where they provide GPP, or add units with these great people's names), but you would need to edit some buildings to allow these specialist anyway for them to be of any use. What I did was just edit a few buildings to provide the points (actually, I did copy the specialist file too, because I wanted each great commander to be able to add +2 xp to the city's units, but I didn't make a great spy unit or make any buildings allow for cities to assign citizens as spies).
To actually make the building provide espionage points, add a fourth (<iCommerce>1</iCommerce>) (the number is of course, how many points it should provide per turn) line to either <CommerceChanges> or <ObsoleteSafeCommerceChanges>. (I think the first one is for food, the second hammers, the third gold, and the fourth espionage. You need to add these lines with 0's in them if you don't want it to provide anything in that category in order to add some points in a letter category.) I did this for several buildings like inns, taverns, thieves guilds,the Tower of the Eyes, the Council of Esus, and the Sidar and Svartalfar palaces, and the Eyes and Ears network. (in increasing number of how many points)
If you only want passive espionage, then you are done. If you want some units to be able to do active missions, then you need to give then the ability. To do that, all you need to do is change the value next to <bSpy> from a 0 to a 1 for these units (you may also want to chance <bCounterSpy> to a 1 for a few units like lightbearers or other "spies" so you can catch rival "spies"). Also, you must make sure that they are invisible units; if the rival can see the unit, then you can't pull of any missions.