I’m with you. As a computer programmer, I can see God reusing DNA “code” to genetically engineer new species that, while bearing some resemblance to prior species, is not related by descendancy. That is why you get an infinite number of “from a common ancestor” species but no proven direct ancestries, not even recent ones. The evolutionary tree is all leaves and no trunk or branches.
God was never in a hurry.
Psalm 90:4 For a thousand years in thy sight are but as yesterday when it is past, and as a watch in the night.
2 Peter 3:8 But, beloved, be not ignorant of this one thing, that one day is with the Lord as a thousand years, and a thousand years as one day.
I, too, find our re-use of program libraries similar to what we see in the archaeological record.
If I may extend the analogy, you know how every now and then you do a completely new version that requires a lot of code changes? There might still be some holdover code from a decade ago, but at the same time moving from version 1.3 to 2.0 often has a lot more changes than when you moved from version 1.2 to 1.3.
That's what I see with all of these large gaps in the fossil record, including when some "transition species" appear in the record in the wrong order. Evidently God is both very patient and is the same Creator a few thousand years ago that He was a few billion years ago. But at the same time it looks like He every now and then does seemingly miraculous work in making a species or phyla jump in the tree of life (as biologists describe it, not the garden of Eden tree of life). There's enough of that where it's hard for me to accept God's hand in creation from a deist perspective -- the belief that God set up His creation with all the mechanism to produce speciation and then just sat back and watch His work create itself.
The fossil record seems to show God's hand appearing every now and then over billions of years that span creation days 5 and 6.