Yeah, as far as I can tell, you could update all the mods that have updates (Obviously, stuff like Thermal Expansion is a little different), and it'd still break your world. It's one of the reasons that it's taken so damn long to get it done. And, to be fair to Mojang, I think that the last thing that had a visible benefit was the introduction of item transport mechanics. It's possible through any number of other mods, but hoppers do work very well, and it lead to Extra Utilities.
Back to the original question regarding the filling with water, you're kind of on the wrong pack. Anything in 1.4.7 would have redpower, which had it's grate, which would do what you want. In 1.6, buildcraft brought it's drain (possibly different name) in, which does the same thing. But there isn't really any easy way of doing it on 1.5. Just the luck of the draw, I'm afraid.