Congratulations on getting the engine in. For what it is worth, I put the engine and tranny in as a unit. I also had installed the headers before placing the engine. I had to 'trial fit' about three times before I got the brackets all lined up, by the third time, I had it down to a science. (3 floor jacks did the trick for me) Two under each control arm and one to position the nose of the tranny as I slid it under the car.
I'm still not sure how the intake is going to clear the brace between the shock mounts. Are you going to position the engine so the intake is above the brace?
Mike