Those shocks are valved and sprung to use a linkage system. The linkage system serves a few purposes... one is to make the position of the shock correct.
They're not designed to work laying flat out. (This applies to most jap shocks. Some bikes are different though...Buells, for example, ARE designed that way on certain models).
If you look at yours it will move in an arc in compression pivoting at the front and lay more parallel to the ground. This is going to be problematic in terms of performance.
Secondly, they give a mechanical advantage so that the compression force from the movement of the arm is translated via linkages to a correct ratio at the shock.
It won't be impossible to ride as is, but it won't handle nearly as well as it could.
There's a lot of articles on direct mounting like this at:
http://www.customfighters.com
The problems people have aren't so much from bad alignment as they are from using a shock that's not designed for direct setup.
You could try finding a different spring to set it up for direct input, or you could do what most guys do and just get a shock from a bike that is already set up that way. Try the FZ6R setup.