Ok, is this the turbo you have. This is my S15 t28 aka, Garrett GT2560R. These are pics of what your exhaust flange should look like. They shouldnt be threaded. If so, then somebody had tapped them for some reason. There should be 4 studs in the exhaust manifold flange where the turbo bolts up, these 4 studs should pass freely through the holes in the turbo flange. If not they should be drilled so that the studs do pass throught them freely.

Is this the turbo you have?

Notice the bolt holes arent threaded.

Notice theres plenty of clearance between the flange and the housing for the studs/nuts.