A. Not only did the systematic clearing of forests in the United States create farmland (especially in the Northeast) and gave consumers relatively inexpensive--->not only, but also should be used with things that are similar in nature; here you have two positive aspects of deforestation listed first and negative aspects listed later.
houses and furniture, but it also
B. Not only did the systematic clearing of forests in the United States create--> not only, but also --same as in A
farmland (especially in the Northeast), which gave consumers relatively
inexpensive houses and furniture, but also
C. The systematic clearing of forests in the United States, creating farmland (especially in the Northeast) and giving consumers relatively inexpensive houses and furniture, but also --> incorrect sentence structure, but also cannot stand alone in the sentence
D. The systematic clearing of forests in the United States created farmland
(especially in the Northeast) and gave consumers relatively inexpensive houses and furniture, but it also --> is correct because first you see the two positive aspects of deforestation, then two negatives are listed and the two parts of the sentence are combined with BUT
E. The systematic clearing of forests in the United States not only created farmland (especially in the Northeast), giving consumers relatively inexpensive houses and furniture, but it---Needs 'also' to make sense of 'Not only' used in the first part of the sentence