Remove the transmission and try again. Bolt the transmission to the engine. Remember to reinstall the dipstick tube when you get to that bolt. Still, even if you don't own them, you'll find tons of uses for extension bars so it might be worth the investment to get a bunch. Reinstall the crossbrace.
Chances are things have shifted just enough to make aligning the brace a real pain in the neck.
If it just won't line up right, try pushing the transmission a little to the left or right. Don't forget to install the mount bolt in the center of the brace. On the transmission side, you'll see that one bolt is longer than the other. The long one is for the passenger-side. With all of the structural components reinstalled, it is now safe to remove the transmission jack and the jackstand.