There are some simple fixes for a couple of your problems.Slapping the hull:
You simply have the pedals adjusted too close. Just put them forward another notch until you can't smack them into the hull. This goes for any Hobie Mirage Drive kayak. You will not loose power; your shorter stroke is compensated by your faster cadence. Since your legs are less bent you will find you also have more power and less fatigue.Non adjustable seat:
The seat can't go forward without covering the center hatch. Yet it is so large, I use a boat cushion on the back (which is adjustable BTW) as shown below.
I use the i-comfort seat (seen in the pic) as well, but you can ignore that.
An additional benefit to the seat-back cushion is that the pedaling position improves yet again by moving forward another notch, giving a little better leverage with the pedals.
The Drive is not designed to withstand submerged structures, period. Pull the Drive and paddle or pole. There shouldn't be a problem. You can adjust your paddle technique to accommodate the high gunwales by swinging your pivot point. I don't believe a longer paddle will really solve your problem as well as a technique change, but you can experiment.
I agree the rudder is extremely sensitive. There is a lag time also, which makes it even more challenging (a tendency to over-correct). You will learn to anticipate it's actions. If your rudder system is properly adjusted it should be easy to operate and stay exactly where you put it. Take the time to learn how to center it and adjust the tension to get the results you want. Shown below is a track of about 4.5 miles that I ran with the PA while adjusting the rudder only once (doing a 180 at the dam at bottom). The boat lean-steers reasonably well and that's how I maneuvered. I admit this is not practical, but mention it here only to demonstrate that the rudder has sufficient authority to stabilize the boat's direction and can be mastered.
This boat is a little different than you are probably used to. Learn to use it to your advantage and it will serve you well!