Your 5/16 lift on the passenger side of the engine is actually helping the clearance issue by lowering the header a small amount.

You could gain a bit more space at the header by lowering the left side of the engine a small amount. Is there enough meat in the motor mount bracket to slot the holes where it bolts to the block? It would not take much as the header will move more than the bracket is moved on the block.

Keep in mind that the header side of the engine will be lifting up under acceleration so you need to have some vertical clearance above the header.

I was just reminded that the manifold side of the A-series lifts at launch when I broke the motor mount at the Astoria autocross a few weeks ago. Broke one of the Rover polyurethane mounts with a stock 1200 motor. Go figure...