The first point that must be made clear is that the design was purely experimental.
Literal
Make-clear must [possessive-の] first point [topic-は], that design [subject-が] purely experimental thing [copula-であった] [quotative-という] [nominalizer-こと] [copula-である].
Dense academic register. 明確にする = 'to make clear.' The whole left side (明確にしなければならない最初の点) is a noun phrase modifying 点 with an embedded 'must-be-made-clear' clause. The copula であった is the past plain form of である, used in formal written Japanese instead of だった. The pattern ~ということである marks the right side as a statement summary.