I've sent off 2 boats into the Atlantic, and retrieved one of them (the other was found by lighthouse keepers in France).
To answer you specific questions:
I've no experience of ardu-pilot. But tuning the rudder control is a nightmare, and I still haven't got it working as well as I'd like. There are too many variables for any sensibly simple control system. Wind direction and strength, waves, (which not only bash the boat off-course but can also upset the compass reading), trying to use as little battery as possible, heel, to name the ones I've thought of. But overall as long as its going in more or less the right direction its probably good enough. Perhaps an AI tuning system would be the answer, but that's beyond my skill level. (Or interest)
I don't know first hand about surviving real sea conditions: I just build it robust and keep my fingers crossed. One thing though is to avoid fighting the ocean: you probably won't win. Instead, allow the rudder and sail to be moved by waves before anything gets damaged or broken. Eg a torque-limiting clutch on the rudder, and some sort of spring release for the sail sheet. At some sea-state the boat will be knocked down, so just allow that and get back up again for the next wave. One thing that confuses lots of people though is how to cope with big waves. I don't think these are really a problem as they rarely break out in the open sea (waves break at beaches because the water gets shallower) so a large wave is like walking over a big hill. you are going to twist your ankle on a small rock, not because you are on a big hill. Small waves of the size of the boat will cause it to veer off course, or my boat gets hit on the side of the hull which knocks it around. At some point the sea will be too rough for any progress, just live with it.
Make sure your boat is self-righting!!!
My boat has been returned by helpful fishermen several times. Sometimes after it was disabled, but irritatingly sometimes within 24hrs of launch when it was going OK. So put signs on it telling helpful people what to do.
If you can, do a test with your finished boat submerged in a tank of salt-water. You'll need a decent size tank for your boat, and lots of salt, but it might show up corrosion and leak problems whilst you still have time to fix them. Probably for over a week.
1) you need to do trials to see what size sail, and keel you need. Make sure the wind is a realistic strength for the Atlantic conditions. I found that the best sail was much smaller than I originally expected. Keel drag isn't going to add much to the hull itself if it is a reasonably streamlined shape, so put enough keel on to keep the boat upright enough in what you estimate is the strongest wind that you need to cope with. I've decided there is no point rigging for more than force 5 as the sea will be too rough to make any progress anyway. My boat probably goes best in Force 4 (but only tested on a pond, so not much in the way of waves). You need more keel to make progress into wind as the sail will be in tight, than you do across the wind, so into wind sailing probably determines the keel size. I've recently increased the keel to get better into-wind performance as across-wind is good enough. (Ie the boat more or less reaches the maximum hull speed.) I'm not sure the answer on this, but make sure the centre of pressure of the sail is correct relative to the centre of lateral resistance. If the sail is too far back the boat will just weathervane into wind and be a pain to steer. Too far forward and you'll struggle going into wind. Do some early trials on mast placement before you get too much else fixed. And if you then alter the sail, the mast may need to be moved.
2) I've used 2 different methods for rudder control waterproofness. First was to put the servo in a waterproof box inside the hull with a sealed shaft coming out, then a push-rod to the rudder lever. This worked well I think, and it puts the seal in a protected space. Second method was to use a magnetic coupling between the waterproof servo box and the rudder shaft. This is more likely to be waterproof as the wall of the box isn't compromised at all, with magnets inside driven by the servo and outside on the rudder shaft. It is a bit sloppy though, but has the advantage of not allowing too much wave force on the rudder to drive back to the servo. I changed design because the second boat has a sloping rudder shaft that putting a crank onto looked very ugly and couldn't be hidden in the hull. So make sure whatever design you use that waves on the rudder can't back-drive and damage the servo. People have used various types of torque-limiting clutch, or spring loaded drive rod. Also, put some sort of a skeg in front of the rudder, so that any obstructions don't hit the front of the rudder and bend the shaft. Best if you can to support the rudder shaft at the bottom rather than cantilevered (although my first boat didn't have this). NOTE that I don't waterproof the entire hull, I use waterproof boxes and custom waterproofing for the bits with anything electrical in eg PV.
3) Very difficult to do any analysis on solar panel positions I would think. I've just put them flat recessed on the deck. Too many variables with sun angle, boat heel, shadow from the sails (as mentioned above) etc. Make sure they are waterproofed as sea water plus electricity is a very good corrosion enhancer. Get as many on as you can. Regarding electronics to optimise the power point etc, I tried out some and although they do improve power in certain conditions, they can also make it worse. So in full sun there is an improvement, but in low light the chip wastes more current than it gains. Since in full sun I think I've got enough power anyway I removed the chips to optimise low-light conditions. I have just chosen PV cells to have a volts or two more than my battery to allow for volt drop through the regulator. (This also gets the PV to run near is best power point.) Volt regulator is set to 8.3V for a 2cell Li battery so no complicated charging. Just rely on the limited current from the PV to avoid charging too fast. This is at least simple even if not perhaps the ultimate optimum, but I didn't want to spend too much time on a PV charging circuit.
Good luck
Phil Smith