Welcome to the forum first off.
The water pump housing is the same for all the B and RB blocks, so no reason why it wouldn't fit, even the industrial engines have the same mounting locations and as far as I know, shouldn't be different than car/truck engines (there is a water hose connection on the front of the heads for cooling sometimes, instead of a freeze plug), so, unless it is the timing cover itself, can't think of any reason why it wouldn't clear. With that in mind, have the surfaces been machined in any way, or do you have access to a different housing? The only thing I could possibly think of would be the engine was set up to have an engine plate mounted to the front of the engine, where they take a plate and bolt it to the front of the engine and the water pump mounting face is used as the mounting location and then the water pump housing would be shaved to ensure all the pulleys line up properly, but that would be a rarity, something you might find with a boxed engine that was a project for something else? This might be done if the engine came out of some form of industrial application, too. Timing cover isn't aftermarket or anything, is it? What year is the block itself? Probably easiest to get a replacement housing, they don't wear out very fast, and like I said, B and RB are the same.