QQ there are two reasons for gaps.
One is that there may have been periods of rapid evolution which didn't have enough time to leave significant geological traces for all the intermediate forms. Another is that the fossil record IS incomplete. Not every form of life that ever lived was preserved. Some fossils have been destroyed over time, and not everything has been recovered, nor will we ever find every fossil of interest that happens to be in the ground.
Nevertheless, there have been transitional forms found between almost every major group. They have been found between fish and amphibians, between amphibians and reptiles, between reptiles and mammals, between reptiles and birds, etc. The whale series is full of transitional creatures as are other lineages.
Even today we have reptile-like monotreme mammals that lay eggs and have a milk patch instead of nipples, and a single hole for excretion and reproductive purposes (a cloaca, like reptiles). These are the platypus and echidna. They lie somewhere on the continuum between reptiles and mammals, but they are classified as mammals due to their hair, warm-bloodedness, and milk production.
I believe when the Bible says God said things like "Let there be light" that it could refer to things that took longer than a single moment.
If we believe that God created the universe, then we must be able to look at that universe and draw meaningful conclusions from it, otherwise all of science is void. We know the scientific method works, and is not void, because of all the advances it has brought us.