Is it possible that the manifold came from an older grill? If I recall, the angle of an older cookbox is slightly different and will pitch the manifold a little.
Well, now I don't think so...
I was out in the shed playing with stuff today and I took a few pictures. First, I think it might be pretty hard to put a 1000 manifold on a Silver (and vice versa). I didn't realize this but, the Silver mounting bolts are about 3/8 inch closer together than the 1000. In the picture below, titled "width", you can see the difference.
Next, I took the head off my little square and, best I could, tried to note the difference in the two angles. The 1000 is pretty near 90 degrees (probably is 90, give or take for the rust). The Silver is less than 90 (from the bending perspective - bent less than 90). This is the angle difference I was referring to in my (quoted above) post.
I'm thinking they made the change to eliminate the cast-in wedges on the 1000 cookboxs (maybe saved some cost? ) . The wedges make up for the slope in the cookbox wall - resulting in a horizontal manifold. The Silver cookboxes don't have these wedges so they just bent the mounting tabs on the manifold a little less to accommodate the slope - and still have the manifold end up horizontal.
I don't have any older Spirits (like the 700) at the moment but I'm wondering what they did on those grills. Did they have the cast-in wedges like a 1000? Are the mounting bolts the same width as a 1000? Or, are these aspects the same as a Silver? As Hank has said before, it looks like the Spirit cookbox was the predecessor to the Silver - while the 1000 was totally dropped.
Sorry to have geeked out here

- I find this kind of mechanical history really fascinating...