Answer to question 1:
The spellings differ in the paragraph in the sense that they were adapted so that the word would "look the way it sounds". For instance, we currently spell "together" and not "togeather" since the letter "a" does not represent any phoneme and, as a consequence, is not absolutely necessary for the word to be read and pronounced properly.
The same happens in many other cases in the excerpt - wisdom X wisdome; halfe X half; difficulte X difficult; equal X equall; own X owne.
There are also words that have been transformed greatly, such as is the case of "espetialy", which was adapted to "especially". This word comes from old Latin, when the letter "t", if used before the letter "i", sounded like a "c". Hence, the transformation.
Answer to question 2:
As for the punctation, we can first address how often the ";" is used where, nowadays, we would most certainly use a "."
For example:
But that which was most sadd and lamentable was, that in 2 or 3 moneths time halfe of their company dyed, espetialy in Jan: and February, being the depth of winter, and wanting houses and other comforts: being infected with the scurvie and other diseases, which this long voiage and their inacomodate condition had brought upon them; so as ther dyed some times 2 or 3 of a day . . . ; that of 100 and odd persons, scarce 50 remained. - This sort of punctation makes the structured idea longer.
We can also note the use of ":" to abbreviate the word January in the excerpt above.
Answer to question 3:
This paragraph is describing the challenges colonists had to face when settling in Plymouth Colony. As often happened at the time and as a consequence of the tough conditions, colonists began to complain and many of them fell sick and died. The very few ones who did not suffer from health issues very bravely and willingly worked even harder in order to help the others.
