If a President had the authority to overrule the judiciary system, that would be the en of democracy, he would not have to follow any law, nor would his friends, the government, etc. and there would be no limit. Some people would be subject to the law and some wouldn't.
You are absolutely right the President as the top of the Executive branch can't overrule the judiciary which is in the Judicial branch of government whose top position is the Supreme Court. He can shut down the DoJ because the DoJ is not part of the Judicial branch of government and the USAG, Jeff Sessions, is the top member of the DoJ. Notice that the AG is not part of the judiciary either but falls under the executive.
The President would have to still follow the law because things like perjury are impeachable offenses. So far I haven't seen anyone throwing any claims of perjury around because if they did the howling would be far louder than it is now. Listen, I don't have a dog in this fight simply because both Donald and Hillary are both far and away too authoritarian for my liking which gives me some objectivity the rabid blue and red teams don't have. That said talking to the FBI guy over dinner about an investigation isn't going to reach the level of perjury because it wasn't part of the official investigation regardless of what was said. If it had been part of the official investigation there would have been a stenographer sitting in the room recording the whole thing or a video recording and we wouldn't even be discussing who said what because we'd just look at the official record. That's why so many cling to this notion of "obstruction of justice" meme. Frankly I'm not sure Donald is actually smart enough to know he could have simply told Comey to shut the investigation into Flynn down but he didn't.
Not if he himself is implicated, and until this investigation has run its full course (which is very much hasn't) he is under suspicion as a consequence of some very clear established contacts with Russia that fell far outside the purview of anyone with nothing to hide.
You say he was implicated and under suspicion yet Comey himself said Trump wasn't under investigation of a crime and that "there was not a counterintelligence investigation of Mr. Trump". I get your rage but there's still no evidence of a crime.
If he's got nothing to hide, the latest 10 years worth of unredacted tax returns would help quite a bit
I'm sure there are both red and blue team members working at the IRS and I'm equally sure a fair number of them have pulled up Trump's tax returns out of curiosity yet they haven't been leaked even given the governmental agencies are a sieve at this point. There must be a Lois Lerner acolyte still at the IRS or perhaps a stodgy version of Reality Winner or even a Snowden. I'm equally sure that eventually they'll come out and they may likely be embarrassing but I doubt you'll find the smoking gun you're so eager to find in there. At worst, we'll find out just how good his accountant/lawyers really are at hiding money but don't expect a 1099 that reads "income: Putin, fellatio".