So, you hammered on your original header. Then hammered it some more. Then HEATED it and hammered the ever living crap out of it again.
And now you're surprised it's different from the new one by an 1/8"? Uh, MAP gas. Bet it wasn't before. I'd have been surprised if it still sat on the table the same as a new one. The tubes are setting that height you're measuring, and you beat the stuffing out of the tubes.
The problem is your engine mounts are like twice the size of the originals. Seriously. These are yours...
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This is a set of originals...
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The originals are 1" thick or less. And they're rubber, so they'll compress even further with the engine weight. Your poly mounts appear twice as thick, and they won't compress with the weight of the engine. All of the mounts all angled too, so they're not just lifting the engine, they may be shifting it from one side to the other as well.
You need to do something else with your engine mounts. Not only will they mess up where the headers sit, they're going to raise the front of the engine. That will also change the angle on your transmission, u-joints, and driveshaft. I really don't think the header is the issue here. It's a symptom of the larger problem, which is the engine being in the wrong spot.