If you're considering purchasing Midwest's kit you should probably just ask them all these questions. Different systems use different parts, and I don't know exactly what they use in their kit.
Typical coilover installations do involve removing the old spring perch and installing a threaded sleave and a collar for the new spring. I _don't_ have Midwest's coilovers but for my set I cut the old perch off with a sawzall. It's not too hard to cut in a way that splits the band for the old perch and doesn't damage the strut tube. Grind off the welds so that you have a smooth tube.
I welded some rings made from exhaust pipe material so that they sit just on top of the swaybar mounts on both the front and rear struts. The threaded sleeves sit on top of those rings. Some people leave the sleeves loose, which won't really hurt anything but makes it a little hard to adjust the ride height. In my case I had unknowingly started with "fat" strut housings which required some threaded sleeves with large i.d., and I still had to shrink fit them onto the struts (sleeves in oven, struts in freezer, put 'em together and let 'em get cozy with each other).
