The keelson is already too short so there would be no sense in saving any of it to use on another attempt at the same plans.
I think you can resurrect what you have, though the boat would be like 6" shorter. It couldn't hurt to try if you're going to throw it away anyways.
In the middle photo where it's looking down the stem from the bottom, the reference point is the line drawn on the edge of the stem. The point of the chine is set back maybe an inch and the point on the sheer is set forward maybe an inch from the line on the stem. That is not right, the points should theoretically meet on that line. That's where the apparent twist comes from. It's hard to tell exactly how the joint between the stem and the chine and sheer is to be done, but the point is they should meet and the ends be both in plane with that line which is set by the 42 degree cut.
So, if you cut and shorten the sheer clamps to where they will join and be in line with the chines on the 42 degree angle, that should bring the faces of the chine and sheer in line so ply will lay flat on them. The stem will be have to be cut and will end up narrower, but if it is too narrow, you could just glue and screw a piece on to bring it back to it's original 3 1/2" width. Of course you'd also have to shorten the strong back too.
Another thing is that 42 degree cut. The plans are somewhat strange in the way they give measurements and angles. The stem is to be cut 42 degrees, but when it's attached to the keelson, the rocker of the keelson will add a degree or two. They give a measurement of 3 3/8" cut on the end of the strongback to give you the angle to cut it, which is bogus, they should just give the angle of 44 degrees or whatever it is and be done with it because any variation in the width of the 2x4 strongback will give a different angle with a 3 3/8" length cut. So since you used particle board for the strongback, maybe you just cut a 42 degree angle on the ends of it and that would also tend to throw off all the joints of the stem/chine/sheer.