There is a donut gasket that goes inside the flange area. The Fiero Store has the donut and the bolts and springs that are needed.
https://www.fierostore.com/Product/Detail.aspx?s=54501&d=388&p=1Misalignment can be caused by several things. The lower part of the exhaust has springs that suspend it. They could be pulling or the lower exhaust sections could be bent or out of position due to removal of the converter and rewelding out of position.
Bad transmission mounts can cause it to be out of alignment, too. The upper Y pipe seldom gets bent so it's probably correct. When we put Aerodonamic back together, we had to loosen the Y pipe at the exhaust manifolds, install the downpipe bolts and springs then pull everything together.
BTW, NoMad is looking for the ESC Knock sensor if you're not using yours.