The key is that "two days" is a measure and measures are treated as singular.
That is why your option 1 works as the subject, verb, and predicate are in agreement. However I do not believe it needs a hyphen
X was Y, or X were Y ?
Can a singular be a plural? Not often. X and Y are either both singular or both plural.
John was a champion, not John were champions.
If we choose "It" we must choose "was"
Next ... do we need an "a"?
If you chose a singular subject "it" you're going to compare it to something singular.
- It was a X : if X is a noun,
- It was X : if X is an adjective
Why can "two days" be singular?
Well a "dozen" is a singular... it is a unit.
but, you might say "Two heads" are better than one.
.... there "two x" is plural if X are thing(s), not a distance or measurement.
"Two days" as used in the predicate is singular because "two days" is a measure (measuring a span of time). That lets "two days" agree with "it".
~ a ~ measure.. Measures are treated as singular nouns so you would us an "a". Other examples:
4 hours is a long time to wait
The height difference between Mary and Jan ~is~ (not are) two inches.
Tommy is two heads taller than Lisa (haha, if you use 'heads' as a measure it changes things from the plural "two head" used as a subject!)
"tough" and "first" are simply adjectives referring to the span "it/two days".
With that explanation option 1) , the way we commonly hear it, is indeed grammatically sound - however the hyphen is not needed as "two days" is the measure, and 'first' is an adjective modifying the measure.
It was a tough first two days
Option 3) of yours does also work.
It refers to "days" as individual time periods !
A plural "they" , the plural conjugated "to be" as "were" and "two days" here meaning two individual days.
They were tough first-two days.
That would mean something ever so slightly different.. ~each~ day was tough.
Also, it may emphasize that the "day" as in the part of the day when the sun was up, were the tough parts rather than the 24 hour meaning.
The "first-two" as an adjective feels awkward in this plural and I'd be open for more input on the use of the hyphen. Without a compound adjective this 3rd choice isn't awkward at all:
"They were tough first days." isn't awkward.