It’s been two days since the Justice Department was thrown into upheaval after senior officials made the unorthodox decision to overrule Roger Stone’s sentencing recommendation. The spectacle of political appointees intervening to help one of President Trump’s biggest allies has resurfaced very serious concerns about the politicization of investigations.

The four career prosecutors on the case soon moved to withdraw from it, while the former U.S. attorney who oversaw the case had her nomination to a Treasury Department job withdrawn — shortly before her confirmation hearing, no less.

Attorney General William P. Barr offered his first public comments on situation Thursday in an ABC News interview, confirming that he personally decided to overrule Stone’s recommended sentence of seven to nine years. Barr, though, said he made the decision before Trump tweeted about it Tuesday morning and repeatedly urged Trump to knock it off with the tweets.

Many questions remain unanswered, though. Below are the biggest ones.

1. Why was this so important, given the bad optics?

One thing we have learned about the decision — at least according to how Barr has described it — is that it was made before Trump tweeted in the wee hours of Tuesday morning that the recommendation was too harsh.

There’s a reason Justice officials have clarified this: Because it looks less like the Justice Department was acting on Trump’s marching orders. Trump has also said he didn’t specifically ask it to take such an action (even though he claims that’s his right).

But just how long before? And if the decision was made Monday, after the initial sentencing recommendation was filed, then why was it not disclosed until Tuesday, after Trump tweeted?

Trump has also made little secret of his feelings on Stone’s case, saying repeatedly that his ally had been treated unfairly. “I think it’s very tough what they did to Roger Stone, compared to what they do to other people on their side,” Trump said on Christmas Eve. He also scoffed at the idea of sending Stone to prison for years in a November tweet.

So it’s not like officials even needed the Tuesday morning tweet to know what Trump desired. It’s exactly the reason presidents like Trump are discouraged from commenting on ongoing criminal matters: Because it raises the specter of them trying to influence those matters.

And even if there was no direct influence from the White House, this was still a top political appointee intervening to help a presidential ally — when he didn’t have to. Barr needs to be asked why he thought this was so important, given the appearance of it all, which is bad even if you divorce this from Trump personally.

2. How on earth were senior officials “shocked?”

Another key and perhaps questionable part of the Justice Department’s explanation here is that senior officials were somehow “shocked” by the sentencing recommendation — and that this whole thing stemmed from a massive miscommunication.

“That recommendation is not what had been briefed to the department,” a senior Justice Department official said Tuesday, speaking on the condition of anonymity to discuss a sensitive case.

As The Post’s Justice Department reporter Matt Zapotosky noted on Wednesday’s Post Reports podcast, though, that’s difficult to swallow. There were extensive discussions about the recommendation in the days before it was filed, with career prosecutors pushing for a harsher sentence and more senior officials disagreeing. How is it possible that a final recommendation that was within the guidelines — however harsh — would have been a surprise, much less a “shock?”

What’s more, why the need to intervene in this case, given prosecutors are generally allowed to make such guidelines-based recommendations?

It just doesn’t make much sense at this point.

3. Has DOJ done this for a non-Trump ally?

It’s a question The Post’s team posed on Tuesday, but didn’t get an answer:

The official could not point to another instance of Justice Department headquarters overruling and replacing a sentencing memorandum a day after a filing but insisted it was not unusual for law enforcement officials to “correct the record.”

It would sure be good for the Justice Department to pin down when this might have happened in the past. If the Stone case is as exceedingly rare as it seems, that makes it more difficult to believe there weren’t politics at play here, on some level.

4. Does the Michael Flynn situation play into this?

Speaking of the above: It’s clear this is unusual, to one degree or another. But what if it’s not even the first time there’s been such an intervention to aid a Trump ally?

Last month, prosecutors recommended zero to six months in prison for Trump’s former national security adviser Michael Flynn and wrote about his offenses in harsh terms. Then, a few weeks later, they followed that up with a filing that took a very different tone toward Flynn and said a sentence of probation would be “appropriate.” (The initial sentencing recommendation hadn’t even mentioned probation.)

It wasn’t quite as stark as reversing a sentencing recommendation, but it turned more than a few heads at the time. It may turn out to be a pure coincidence that the language on Flynn was scaled back, but it’s certainly fair to ask questions about that situation, too.

5. The Jessie Liu question

The withdrawal of the four prosecutors on Tuesday was the big headline, but next was the decision to pull Liu’s nomination to a Treasury Department post. She had been the U.S. attorney overseeing the Stone case but was replaced by a top Barr ally two weeks ago. Liu was nominated last month to a Treasury Department position and took an unconfirmed job there while awaiting confirmation.

And then that nomination was pulled. The most obvious potential reason: She was slated to testify Thursday, which is not great timing with everything blowing up in the Stone case. Trump had also been lobbied by allies who argued she had mishandled Stone’s case and other matters, The Post reported.

But if it’s more the former than the latter, it suggests there is real concern about what might come out of having someone put under oath — which doesn’t exactly speak to this all being on the up-and-up.

6. Does anyone speak out?

We’re not hearing from Liu today, nor have we heard from the four prosecutors since they withdrew Tuesday. That may not be a huge surprise, given three of them remain employed in the Justice Department and aren’t empowered to give interviews, but one of them — Jonathan Kravis — has resigned from government entirely and could ostensibly speak out.

The decision has also so thoroughly roused concerns in the legal community that you have to think there might be some people internally who’d like to say something — even anonymously. Of course, coming forward these days isn’t a terribly attractive prospect, given what we’ve seen on the Ukraine whistleblower and Lt. Col. Alexander Vindman.

One way or another, though, we’ll probably learn more. And answers are certainly needed.