The installation validation will not make any changes to your RTW/EB installation, just check how it looks.

Perhaps you should try to move the eb\data\packs\mod_1.pak file to somewhere else and start the game to see if it resumes normal operation then. I do not know the contents, but I guess that this is the vanilla water you added back in. You say you do not think it is the cause of the CTD, but it appears to me to be two entirely different issues.

The fact that you get the on-load CTD with normal RTW means that this is unlikely to be an EB issue. I suggest you get that working first, then try EB again afterwards. You could ask for support from CA, I have no experience with them though. Perhaps an upgrade or downgrade of your drivers would make a difference. Can you remember any other changes you have made to your system from the time it worked, beyond installing the vanilla water?