The HP2 mounting holes are spaced further apart than on an a4. Which is why you would need to swap the uprights to use the s4 front brakes. The tip s4 uprights will work on your car just fine, they're all the same. Auto, or manual, it doesn't make a difference.

96-00 1.8 a4's used a smaller outter cv. In 01' they switched to the larger v6 sized outter cv's. As long as the uprights off the s4 are steel, you can bolt up the s4 uprights without any issues. If they're aluminum you'll need to swap over the front lower control arm with them. The lower balljoint is larger because of the steel insert that's pressed into the aluminum uprights.