Miles does it really matter? Are there really problems? I mean a problem is not a problem if it does not really matter.
The part that doesn't matter is the number of gaps because there's no expectation for any particular number of fossils to be found.
The other pieces of your post involved incorrect starting premises. I posted to point out the problems with those premises.
You stated that fossils are never found repeated in more than one layer. That was an incorrect statement because there are many cases of fossils found spanning multiple time periods.
You stated that in order to be accurate the fossil record should contain fossils of living animals. That is incorrect because the fossil record can be accurate without being complete.
You stated that the fossil record matched a specific flood sorting pattern. That was an incorrect statement because we don't find fossils sorted by habitat or mobility or buoyancy.
Here's the complete mention of the tree trunk in that article, I'm not seeing where you are getting that it was found under hundreds of feet of rock in unreworked surrounding material.
These findings aren't mentioned by evolutionists today, because it clearly falsifies their ideas. I don't know how a 2ft. diameter tree trunk could possibly slip though hundreds of feet of tiny cracks in the rocks that aren't visible or reported by anyone, but if that's your idea, then it certainly belongs to you and nobody else. When we have thin sedimentary layers in salt deposits that extend for many miles, then it normally falsifies reworking as a plausible explanation.
Cotter (1931, p. 299) also made this interesting observation: "About the year 1924 a large trunk of wood of a modern type and scarcely at all decomposed was found in the salt in the upper tunnel of the Khewra mine. Dr. Dunn, who examined this wood states that the trunk was about 2 ft. in diameter, and that there were several branches associated with it of about 3 to 4 inches in diameter. Prof. Sahni regarded this wood as modern and resembling an Acacia now found growing in the Salt Range.
There is no way to get these thin sedimentary layers into salt deposits after the fact. But if these salts precipitated out of solution during a flood, then we can clearly fit it into the model while carrying plants, insects, and trilobites during deposition.
I'm going to try to get back to the original topic regarding the fossil record being sorted by floods and examples such as flowers being inconsistant with that idea.
This is a example of a fossilized flower.
This is a example of a fossilized pollen grain. Pollen and spores and similar fossils are called microfossils.
The paper you link talks about microfossils (pollen, wood fragments, etc.), not about flowers being found (tree stumps are also not flowers). While microfossils could be evidence of flowers existence if they were confirmed to be in-situ, they are not flowers themselves. To make things simple lets say that tomorrow the supposed evolutionist avoidance of evidence of cambrian flowers disappears, and it's announced that there were definitely flowers in existence at the time of the cambrian layers deposition. This still wouldn't change that we haven't found any actual fossilized flowers in cambrian strata and if we are talking about the flood's sorting action on flowers we need to be discussing fossils of flowers, not pollen or other non-flower fossils. When we do find fossilized flowers they are not where the original post says we should expect them as a result of sorting by flood.
If the flood sorted flowers by mobility, their fossils should be found near the bottom of any set of fossils since flowers can't swim or run. Instead we find them above mobile swimmers like trilobites and certain mobile land species.
If the flood sorted flowers by elevation we should find aquatic animals below flowers. Instead we find aquatic mammals above or even with them.
If the flood sorted flowers by buoyancy we should find them above denser objects. Instead we find them below objects like human made stone tools.