What was the main purpose in Japan trying to capture the Dutch East Indies oil fields intact?

In brief, the desire to capture them intact is because Japan needed the production and refining capacity immediately in order to conduct the war in the manner they wanted. They actually had reasonable success in doing so, and restoring what losses there were, but transport of oil products to Japan became the real bottleneck as the war went on.

So, lets look at various bits of information:

One measure of the Japanese capability to refine comes from this Bulletin of The Japan Petroleum Institute article by Shigeki Fukuba, Volume 10 (1968) p. 83-91. Quoting from the introduction:

Petroleum refining in Japan has a long history, but the production and refining of crude oil as an industry began in the middle of 19th century.

Since then, many refineries have been installed and expanded, and modern refining processes were introduced step by step to the refineries, and the crude unit refining capacity had reached to 80,000 barrels a day in 1944. However, 62 percent of refining capacity were lost by air-raids during World War II.

Later it is noted that, of that 80,000 b/day, 57,000 is private companies and 23,000 is from Army and Navy units. Note that 80,000 b/day over 365 days is around 30 million barrels per year.

Online at the Pacific War Online Encyclopedia entry on Oil, they go into some depth on the oil situation, including year-by-year breakdowns of the Japanese oil inventories from 1941-1945. First, though, they note that the Japanese, recognizing their dependence on imported oil, had begun stockpiling it shortly after World War One. By March 1941 the article reports the total stockpile was 42.7 million barrels. Production in the East Indies and Borneo is reported at 65 million barrels (by comparison, US production was 1.35 billion barrels a year). Starting inventories shrink year-over year from nearly 49 million barrels (including crude and refined products) to 38 million in 1942 to 25 million in 1943 to only 13 million in 1944. Consumption is listed as going from 37 million (1941, mostly peacetime) to 42 million, 44 million, then crashing to only 25 million barrels in 1944.

A website at Penn State University suggests that destruction of the oil fields was generally recovered pretty quickly, sufficient to prevent this steady fall in stockpiles:

Within a short period, Japan was able to restore the Balikpapan oilfields with astonishing results that far exceeded their goals. Oil production in the Southern zone in 1940 was 65.1 million barrels. In 1942, the Japanese managed to restore 25.9 million barrels, and in 1943, 49.6 million barrels (75% of the 1940 level).

On the refining side, a paper from TU Delft says that the Pladjoe refinery was captured mostly intact while Soengai Gerong was 80% destroyed, although production resumed within 6 months. By January 1945 these refineries reportedly were producing half the oil and three quarters of the aviation fuel used by Japan.

So it would seem that everything should be looking good - the production was restored, the refinery capacity pretty much restored, so what else went wrong? The answer is the US submarine campaign against shipping. As noted at American Foreign Relations,

The Japanese gained control of the Netherlands East Indies in 1942, but many of the oil facilities had been sabotaged and took time to restore to full production. More importantly, transporting oil from the East Indies to Japan proved increasingly difficult owing to the remarkable success of U.S. submarines in interdicting Japanese shipping. By late 1944, Japan faced serious oil shortages, with crippling military consequences.

This is also noted in the Pacific War Encyclopedia, where it is stated:

Hence much of the production from Southeast Asia never made it to Japan. Although production in Japanese-controlled areas peaked at almost four million barrels a month in 1943, imports to Japan never exceeded about 1.4 million barrels a month.

And:

The last tanker from southeast Asia reached Japan in March 1945.

So, the plan was to capture the oilfields and refineries intact, use them to replace the oil no longer coming from the US, and prosecute a quick war in the Pacific to convince the US to back off and stay away. While the destruction of some of the oil production and refining did occur, these were restored in reasonable time to have not slowed fleet/air operations. By then, however, the transport capacity to Japan itself had been reduced and never recovered. This led to much of the Japanese battle fleet being stationed near the East Indies, fueled often by unrefined crude, keeping them far from the battles in the Pacific post-Midway. It would appear that much of the tanker traffic was primarily aviation fuel, including for the carrier groups (the carriers were kept near Japan).

It is unclear what, if any, additional operations the Japanese navy could have carried out between 7 December 1941 and Midway (4-7 June 1942). By 1943 most of the production and refining had been restored, with the rate of consumption highest for that year by Japan. After that, the losses to submarines meant that less and less of the oil production was reaching Japan - the capacity existed in the East Indies, it just could not get where it was needed. The operation generally succeeded, the war plan failed.