*So as I read it* [& I'm no lawyer] the US DOJ is saying that if Dotcom starts a new service they may file new charges against him -- of course they could just as well file new charges against him whether he starts a new download site/service or not, so that's just a warning shot... AFAIK the DOJ can't be charged with harassment, so they can file charges pretty much whenever they want for whatever they want. They may need a grand jury to indict, but in this sort of situation that may be seen as a sort of rubber stamp approval from a group of people who'll only be told what the DOJ wants to tell them -- they wouldn't decide innocence or guilt, but rather if the DOJ had a plausible legal case or not. Reading the articles in Wired, Dotcom is pretty much expecting that sort of thing, understanding that the head of the US DOJ is a political appointee, and that it's not all about the law, but maybe a means to an end.
The US DOJ is also suggesting that maybe Dotcom lied when he said in his bail application that he couldn't re-start Megaupload, &/or couldn't start up a new version of the service. Lots of potential legal arguments there until Dotcom actually starts to do something [at what point does talking about something become more than just talk?], so again maybe more a warning or threat that the DOJ would pursue this line of prosecution seeking to have Dotcom's bail revoked.
If the Republicans win the White House next month, & particularly if they retain the House & take the Senate, I'd expect both house cleaning & thorough investigations at the DOJ, which over the last 4 years has made a Lot of enemies. There might also be a bit of outreach to NZ, some changes in the way the US wants to be perceived by other countries, particularly allies. Dotcom may or may not come out ahead, but based on the Wired article he feels he'll have a better shot with a new US admin., so will likely want to delay anything too concrete until he sees the election results.