1. When using the general store can you sell as many goods and as many good types as you wish?
Yes. Because this is exactly what the rules say (page 17).
2. On the whaling board can there be 4 or more on a line or does each line only hold three ships.
max. 3 (because the rules say so: "no more than 3 ships can ever be on a space", page 5)
3. Whaling phase. … Do you count out all the tiles for all the lines, create one massive selection pool,
This. Because otherwise the rules would said to do it the other way, and they don't.
4. Tell me I have the end correct.
Yes. E is a loop with 1 movement at a time.