Lowering the rail may be a tricky task. The job is not as simple as shortening the struts. Because of the geometry of the struts, the new spacing between struts will change. In that case you would need to relocate the stantions for the struts and that means the old holes have to be filled and the gel coat repaired. If the top of your gunnels is non skid, the patch job is even harder.
If you try to reuse the original mountings, the top t fittings will have to move on the main rail. The tees may not want to move and if they do, I am pretty sure the rails will have marks where the tees used to be. The hex set screws on the fittings may not unscrew easily or they may pull the threads with them.
On the challenging side of things, removing the old rails and seeing if it could be made to fit with cutoff struts would be an interesting project.
Before cutting the struts, I suggest that after seeing if the rail might fit, get a few feet of railing stock and cut it into the new required lengths. In other words, Do not cut the existing struts . If things don't fit, you will need to go back to the original layout and strut lengths. ( mark the old struts as to where they came from. They may not all be the same length)