You could instead modify the SpreadFactor of Hinduism
Look in the Civ4 assets (not warlords, this file wasn't changed for WL so they did not iclude a copy their, this goes for any XML file that wasn't modified in WL the original from Civ Vanilla is still being used) and find ReligionInfos.xml under the GameInfo folder. Modify this tag on line 15, lower if to slow the spread.
<iSpreadFactor>100</iSpreadFactor>
The SDK is for re-compiling the Dll file found under the Assets folder, this file controls 90% of the game (the rest is found in the un-modible .exe or in the Python files). You need to know C++ to use it, the end result of which is a new Dll file that can be put in a mod to change the way the game functions at the deepest level. Many popular mods use modified Dll's to achive new effects. Try the resent Composite XL mod by Ket to see some of these new effects in action.
I think you should look to python for doing this, I cant give you much advice their but to say that lots of stuff can be scripted in Python which would be difficult or messy to do in the SDK (the reverse situation exists too and many things are just imposible without the SDK). Kael would be a good source of input on these kinds of very specific custom effects.
Your correct you only include the modified files but you must create an identical directory tree for them to be detected properly. When Civ4 is launched the .exe's main function (besides preventing piracy) is to organize other files. It will collect all the files&folders in the CustomAssets directory then it will search in what ever Mod is being run and grab any files not matching what was found in CustomAssets. Then it gets the WL Assets directory and again pull in anything not matching something already found. Lastly it pulls in Civ4 "vanilla" Assets.
And ofcorse the #1 rule, never modify your Original Assets, copy it and make a mod out of the specific file your changing.