You can put the adapter plate/flange almost anywhere you want. Thats good cause it should make your downpipe a little easier to fab. With a T3/T4, you may have to go top mount cause it probably cant fit with a bottom mount setup.
I believe the ports do line up and you can use an SR manifold. Guys did this before SSA started making a KA mani. As structure said, you just have to weld on a KA exhaust flange.
http://www.WasabiGarage.com makes a bottom mount manifold thats puts the turbo it the same spot as the SR, allowing you to use an SR downpipe. But the SR uses a T25/T28 so your T3/T4 downpipe is gonna be different.
I'm pretty sure you can use the SR side mount with a little cutting of the pipes. Toahk used one on his KA-ET. You can find an OEM FMIC for about $100-120 (starion, evo 8, etc), so you might as well go for one of those. Your setup sounds good. You can find a 1g DSM BOV for under $50.