Good pics -- they should serve as sufficient evidence for your warranty claim if you haven't already filed it.
With two cracks in that position, it will be a difficult repair and may not last long. IMO the polyethylene there looks brittle and has some underlying problems. Nevertheless it's definitely worth a shot! I propose dividing your epoxy into 3 different batches to stay within your short working time limit.
First check the bottom of the boat to see if the lower crack has breached the hull yet. If you can locate that spot, I recommend a small reinforcing scab patch there (on the outside bottom) first using about 25% of your epoxy.
After that has set up, you should apply the next scab patch on the inside fairly broad and thick to stabilize it as much as possible using about 1/2 of what is left.
Finally the drivewell crack should be addressed. About 6 years ago Hobie used to send out a free drivewell reinforcing kit for certain early production boats. Your dealer may have one sitting around or he may still be able to order it ( # 81410011). The part you would want out of it looks like this:
It may need a little modification as they were not designed for the Sport. If you can get one, take the last of your Scotchweld, put it in the fiberglass piece and plant the pre-fitted piece on your drivewell crack (inside of hull).
If not, use your remaining epoxy on the inside, but reserve a little for the outside of that crack. Any material you can bond to the inside will help (customized small section of PVC pipe for example).
Best of luck -- let us know how it turns out!