You've asked two questions.

(1) Can "percentage-wise" be used as an adjective.

Yes. "The percentage-wise method of calculating the metric has many advantages."

(2) What's the interpretation of "by one of percentage-wise and optimal gross margin" which is taken from Patent US 7979299 B1.

Part of the issue is that quote has been taken out of it's context. Also, it's missing some of the original punctuation. Here's the original context, as taken from Patent US7979299:

Methods and apparatus for optimizing markdown pricing

CLAIMS(14)

1. A method of optimizing scheduling of markdown pricing for one or more related items at a plurality of retail sites, the method comprising:

for each retail site in the plurality of retail sites, identifying a type of related items based, at least in part on, whether markdown schedules for individual items would be substantially similar if optimized separately;

determining which retail sites from the plurality of retail sites have similar metrics, the metrics identifying which retail sites are equally close to selling out the type of related items by one of, percentage-wise and optimal gross margin, given a current price of the type of related items; [NOTE: emphasis added for this question/answer only]

Note that among legal documents, patents are notoriously difficult to interpret. In fact, interpretations of the meanings of patents are often decided in court within the context of an infringement of patent lawsuit!

When the phrase "by one of" is followed by a comma, colon, or "the following", it might suggest a listing of separate items. But other times, not. Let's consider another sentence which may be a bit easier to comprehend:

• "He can make great food by one of, spicy and hot recipes, to which said patent Section 6 does forth suggest patently patent stuff stuff stuff..."

Now does this mean "spicy, hot recipes" or "spicy recipes and hot recipes"? Since we have a list, it must be the latter. But additional sentence complexity can make it more ambiguous. Practically speaking, the answer could very well depend on what is decided in a court of law.

There is no clean way to parse "More important, ..." strictly as written, but the intent is easy to understand.

A critical point is in the answer you reference:

...the adverbial phrase ‘more importantly’ modifies nothing in the sentence. What is wanted in constructions of this kind is ‘more important,’ an ellipsis of the phrase ‘what is more important.’

(Note that this is a subject with some disagreement, and the above quote expresses one opinion (of many) in the debate.)

If we accept that "More important, ..." is short for "What is more important is that..." then there is no issue at all: important modifies the fact expressed in the that clause.

Consider the following similar sentences:

Finding the treasure is important.

It is important that we find the treasure. (using an expletive it)

If we ask "What is important?" the answer is "that we find the treasure". (Or, "finding the treasure" in the first setence.)

You can also read "More important, ..." simply as:

This fact is more important: ...

"More importantly, ..." doesn't usually modify a verb in the main clause:

We lost the the treasure. More importantly, we lost our friends in the woods.

You didn't importantly lose your friends -- that doesn't make too much sense. Rather, you lost your friends, and that fact is more important than the fact about the treasure.