There's going to be some variation in shaker positioning in the hood from car to car, due to differences in motor mount height, body mount cushion wear, and front sheet metal adjustment.
I have new original type rubber body mounts, and new motor mounts, and the sheet metal is pretty square
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I measured at the rear center of my shaker, since that's the easiest to measure at the same place. The flat flange on the shaker is about 1.25" down in the hole, below the hood surface. So, the shaker stands about 2" above the hood surface there.
Also, measuring between the rear center of the shaker and the edge of the hood hole, I get about 1.25".
As long as the shaker looks pretty centered in the hole, you're doing good. Yours doesn't look too bad as it is. I think you could use a little more room in the back as you thought. From what I can tell your height looks good. There's no advantage to raising it up more than stock.