I would say: you'll see

"have seen" because of "by then" but "see" is also possible.

HAVE is the best choice. will+ (infinitif without "to")

You can use either, with no difference in meaning.

It depends on the situation. You use [SEE] if they will see the results AFTER the project is done. Using [HAVE SEEN] means that they will see results BEFORE. NOTE: With the use of "by then" in the sentence, it should be [HAVE SEEN] ("You will have seen some tangible results by then.") — but if they really will see the results AFTER the project is done the sentence should be, "You will [SEE] some tangible results [THEN]."; drop the "by" at the end of the sentence.