Is there a simple way to draw a right angle triangle to use as a set-square to get my structure properly square?
Yes, build it as a "golden triangle". A triangle having sides of 3 units, 4 units and 5 units has a 90 degree angle opposite to the longest side. The units can be whatever suits you and the scale of your project. They can be inches, feet, 20cm or even the span of your hand. Just measure it out accurately and you will have a 90 degree triangle.
Is there an easy way using geometry to draw a right angle triangle with angles of precisely 90, 35 and 55 degrees?
Construct a triangle with sides of side length ratio 1:1.428:1.743 to whatever size suits you. That will give you the correct angles.
In the instructions you call for using a flexible batten to draw curves. I am a well equipped wood worker and don't know what a flexible batten is. Can you explain what they are?
A batten is a strip of thin and flexible material that you can bend into a smooth curve and will straighten again when the panel pins or other restraints are removed. Supple wood is the most often used material but it can be plastic. Don't use metal except as a last resort because it isn't often completely straight and that will result in unfair curves.
Many of the newer boats we've looked at have the shrouds attached to the deck rather than chain plates attached to the side of the hull. I don't really like this design because it impinges on the deck space and walkway forward. I was wondering why designers like to attach shrouds to the deck rather than the hull. Logic tells me this would only weaken the shrouds leverage on the mast keeping it upright.
You are correct, the loads in the mast and rigging are less if the shrouds go to the hull side. However, if you have headsails that overlap the mast then they have to be sheeted outside of the shrouds. The wider the boat, the wider the sheeting angle of the headsail and the lower the boat will point when hard on the wind. The solutions are to either pull the shrouds inboard to reduce the angle or to use non-overlapping headsails, which reduces sail area.