There are more than 25000 idioms in English. For us non-native speakers, it is a nightmare to try to rely on idioms. So I recommend you always try to find non-idiom related issues. Here the first split is between the use of simple past tense and present perfect tense. Many fall for the present perfect trap because they have rightly learned that present perfect tense is used when describing an event that began in the past and that either continues into the present or continues to affect the present.
In this question, while it is true that California still relies on income taxes and hence its effect can still be felt (in fact, for this reason, it uses present perfect tense in the first sentence), we cannot say that the effect of the increase between 1962 and 2002 (i.e. from 18% to 48%) can be felt in the present. If the sentence replaced 'by 2002' by 'this year', then we would use present perfect. It seems like the test makers deliberately included the first sentence (i.e. before the semicolon) to make test takers feel as if the effect of the tax increase (between 1962 to 2002) can still be felt.
Since we need to use simple past tense to describe an event that started in the past and neither continues to the present nor continues to affect the present, we are left with D and E. Let's analyze D. I am not sure whether we must need "to Y" when we have "from X". I try not to rely on idioms. There is an 'and', so let's look for parallelism issue.
Income taxes increased from 18 percent of the state's general fund in 1962, and by 2002 were 48 percent. This can be split as
(I) Income taxes increased from 18 percent of the state's general fund in 1962.
(II) Income taxes by 2002 were 48 percent. In a parallel structure, each parallel element must make sense independently. Here, in (II), it is not clear what the 48 % is of. While it is common to have ellipsis (omission of words that are understood without being stated) in comparison, it is necessary that each elements of a parallel structure makes sense without other elements. While you might notice GMAT might have broken this rule in some questions, option E do not have such less preferable issues.
There also seem to be a confusion regarding the use of simple past vs past perfect because there is a time marker 'by 2002'. Past perfect tense is used to indicate an event that occurred before a specific date or time in the past. In this question, the increase happened not just 'by 2002' but we know specifically when it started and ended (i.e. from 1962 to 2002), therefore for such specific period of time in the past, we use simple past tense. Please note that you should not automatically think that we must use past perfect tense just because there is a time marker. Consider this example:
By 2010, most people were using emails to communicate. In this example, 'using emails' did not end before the time marker 'By 2010', so we don't need a perfect tense.