So i took a prep course and just wanted to know, is "D" still the best choice to fill in if you are in doubt or run out of time. Also, are the last 2 sections the one that alwyas count on the exam?
You should treat 'when in doubt' situations differently than 'running out of time and having to blind guess' situations. If you have put some effort into a question and narrowed down the contender answer choices, going with (D) or some other letter by default would be silly, especially if you already rejected it. In those situations go with an educated guess between the answers you have not already eliminated.
As for pure blind guessing on questions you are not able to attempt, it's really a matter of luck. Historically, over all test forms, (D) has a slightly higher probability of being the answer than other letters (slightly above 20% chance), but we are talking about minuscule differences in answer choice probabilities.
Keep it simple, pick one letter to use for blind guesses, stick with it and
that it comes up just like people do when betting on roulette.
Many books and big prep companies have been saying pick (D) for years and from my experience teaching I have noticed that most people that have to blind guess at the end of sections go with (D) due to that common recommendation. Given that, and that LSAC does heavy number crunching statistical analysis on test day performance/results, I doubt they have not noticed that pattern. It is not that hard to notice that on every test there are a bunch of answer sheets with several (D)'s bubbled in a row at the end of sections! This is just my theory, but do you think LSAC wants a bunch of people getting inflated scores due to heavy prevalence of (D)'s at the end of sections? I think not. Don't waste time and energy worrying about this issue, decide on a letter and spend your mental power and time getting ready for the substance of the test.