That's basically what I figured you meant, and it really comes down to geometry. There are wizards on here that could tell you exactly what this means, but I'll tell you that you should put them so the are tangent to the swingarm's arc of motion. The reason shocks are generally installed at that forward angle is to transmit the forces directly along it's length. When you hit a bump the swingarm moves in a circular path (due to it pivoting from one point) towards your butt, and the shocks compress and resist that motion, while dissipating the energy from it.
You get the maximum force 90 degrees from the swingarm (this is called a moment arm), which is why the shocks are more or less perpendicular to the swingarm (under compression). Now, the shock is what's called a "two-force member" which means it can't transmit any torques through it. Essentially, the fact that it can pivot around the two mounting points at the end means it can't support any torque and will behave like a shock normally would at weird angles (like the one your setup is at right now).
HOWEVER (and this is big) that doesn't mean the shock can handle the potential for buckling forces. I don't think it is really possible given the small stroke, but the fact that the shock is absorbing forces along a geometry it wasn't designed for (technically close to tangential to the swingarm but gets farther away from 90 as the swingarm compresses, not good) that would be why it doesn't feel right. I imagine it feels sluggish and sloppy on rebound.
You can probably still use them, but give them a once over for bent shafts or cracked seals. I think it would be possible for the odd forces to mess with it a bit. I would definitely move them back to a more "standard" geometric position.
Edit: Just saw the bit about wanting to keep the lower stance. I would do one of two things:
1) Buy shorter shocks. Sucks that you can't use these ones but at least a set that is designed to be short will work awesome.
2) Weld some big posts on there so you can move the mounting point a few inches above the frame