Here I've drawn the true outline in Red, and the rough centre of each pipe (to give an idea of flow) in blue.
As you can see, the join is nearly spot on 45 degrees. Although it's not as sharp as what can be done by creating a whole new Y-piece, I do believe it will none-the-less function better than the unmodified Y-piece and for a cost of some bolts ($11 from Toyota, will pickup on Wednesday morning and install on Thursday) I'm hoping it will be worth the effort.
BTW to any experienced welders, don't slag me off for the huge weld buildup at the join :o