Stones current case is officially listed as related to the Russian conspiracy/hacking case.
Stone just tried to argue in court that his indictment is unrelated to Russia/ties to Trump campaign.
Mueller cites two primary reasons - the Russian stolen emails are the topic in both, and that warrants from the Russian hacker "raid" resulted in evidence relevant to this Stone case.
The judge agreed, the roger stone Indictment remains listed with the related case being :
case 1:18-cr-00215-ABJ (the Russian conspiracy indictment/hackers)
In Manafort's case, much of it was redacted. When one bit was accidentally unredacted by Manafort's crack team, we learned that it involved Manafort giving polling data to a Russian with ties to Russian intelligence (KK).
Similar to Stone, the same Judge overseeing Mueller's Stone work, oversaw that portion of Manafort's case. Much of it is still not known to the public. The other judge with access to some of those redactions, asked about "Treason", so I think that raises eyebrows about what is under the redaction, consistent with this discussion.
Manafort and Stone both appear to not be taking their prosecution seriously, and have apparently intentionally done numerous things to receive harsher judgement in their obviously guilty cases (stone TBD, Manafort is cooked). It was even reported that from legal sources with knowledge of Stone's strategy, that they are simply expecting a pardon. It fits history, Trump, and their behavior.
So while I hope you're right, that he will let them face justice, it's my #1 concern that he will pardon them. That they stonewalled sufficient to shield he president, and he will reward them with a pardon. Nice and tidy...the old "take one for the team", followed up with a "get out of jail free" card.