I presume Trump can order a stop to this investigation the moment he gets in office?

Shouldn't be able to but I doubt it stops him from trying.

I believe the President can't interfere with an investigation. Future Attorney General Jefferson Beauregard Sessions III may decide it's wasting resources or some such not political at all reason to terminate.

Just heard this question posed and answered on NPR. Really it'll be up to new AG Sessions, and yes he can stop it, but it would be politically fraught if he did.

"Politically fraught." Looking at everything going on right now, I would have to ask: "Compared to what?"

Well no he can't. An IG can be removed but a 30 day written notice has given to congress. And the career types at justice can carry on even if he is. The AG has no say.

I think it's patently obvious that the way Clinton handled her email was illegal under the law as written (albeit less serious than things Trump is guilty of). But I also think that the way Comey handled the matter was unprecedented, unprofessional, and baffling, so I welcome further investigation into his behavior. Personally I think he's an idiot and a chickenshit who managed to advance beyond his level of competence, but that describes most of Washington DC.

If she broke the law, she would have been charged. That's been their goal for years.

Not true. Laws get broken all the time without charges being brought, for lots of reasons. There's one set of laws for the 1% and another for the rest of us. Using Comey's failure to prosecute doesn't carry much weight since according to the FBI report and his own public statements Clinton met every standard for prosecution except for intent - but the law as written expressly and (ironically) intentionally does not require intent. His whole argument for not filing charges is that it would set a bad precedent, never mind that not filing charges set an even worse precedent.

It's water under the bridge now, Clinton and her supporters can be relieved that she wasn't charged and still blame Comey for throwing the election (along with the Russians, the Bernie Bros, the Greens, the unions, the white working class, etc, etc).

If he filed against Clinton he'd have to go back and file against the previous Secretaries as well. The precedent has been well set.

No previous Secretary established their own private email server. Rice didn't use email at all, Powell did use some personal email and if there's proof that Powell sent classified-at-the-time information via a non-secure channel, then yes, he should have been charged as well, along with anyone else who did the same thing.

But "but the Republicans did it too" is not a defense.

Did Clinton send classified-at-the-time information? When I stopped paying attention it was still all classified-later information. Did they find something?

Edit: I found that she was using her personal account solely, so there is going to be classified info in there. And that's a big big problem. Using personal email for govt business is a huge issue. But I don't think there's a prosecution here. And, more relevantly, neither does the FBI.

They've spent years of effort and millions of dollars to ruin her rep and deny her the presidency. They didn't hold back from prosecution because of solidarity with the 1%. It was an imaginary scandal, part of their successful effort to depress the vote.
This investigation may be interesting, but Comey will probably never present a coherent explanation for his intrusion into politics.