Super Ikontasmuse front cell focusing - when you focus, you only move the front most cell of glass compares to other cameras where the entire lens moves (or the paper moves ala the Mamiya Six rangefinders). Front cell focusing involves a sharpness compromise either in close or far away. On my SI IV (and normal ones as I understand it) the camera is shaper at infinity than it is when near focused. Mine is very soft when shot wide open with a near by subject and I haven't found a lens adjustment which can fix this.
A few tests to narrow down you issue.
First, when focused at infinity and looking at something really far away, do the images line up? If not, I'd take a look at why before dong anything else. The rangefinder may simply be off.
If it is accurate, I'd move on to checking the lens. Open the back of the camera, and price of frosted glass, tape or something else which will show you the projected image in place against the back of the camera. Set the camera to B and try focusing near and far. When is and isn't it in focus? This should generally match the results you see while shooting. If this looks off , the lens itself may need to be adjusted.
Just keep in mind that something is going to be soft due to the lens design and how they implemented focusing.
Edit: Yes, you generally need to be shooting at a higher shutter speed than smaller formats to deal with camera movement blur or using a tripod. I try to shoot at leat as 250 when possible. Note that different rules apply for the Moskva cameras as the shutters themselves generate shake at the highest shutter speeds.