Wow, you waded into a lot of issues. I agree with some of them, and offer some additional thoughts to consider:
Your opening paragraph seems to suggest that a lot of Federal Agencies don’t follow the “Rule of Law”, probably due in part to Qualified Immunity. On the other end, it has been stated that the average business executive commits 3 felonies a day, because there are so many Federal laws designed to catch anyone doing anything the government deems inappropriate. To paraphrase another P4P poster, “Show me the man and I will show you his crimes”. Federal agencies will claim they are following the “Rule of Law” to the letter in prosecuting any and all cases. The problem isn’t following the “Rule of Law”. The problem is that there are so laws that any citizen can be nab. And with QI, government employees will not.
You suggest establishing an Office of Federal Oversight Investigative Services (OFOIS) to replace the Inspector General’s office. There dozen of IG positions across many, if not all, major Federal Agencies. I presume your proposal is to consolidate all of them under OFOIS, not just DOJ? And to whom would this Office report to? To someone in the executive branch? White House Cabinet position? Directly to President or VP? Let me suggest that it report to the Congressional oversight agency, the General Accountability Office (GAO)
You also suggest “Restructuring the criminal justice organizational chart of the federal govt. to establish systematic checks & balances within America’s criminal justice & intelligence agencies.” I too think this is needed. The entire Federal justice system is housed within the executive branch: investigators, prosecutors, and courts. And they work lock-step with each other to ensure a 99% win rate, no matter how questionable a case might be. Now you might think the Federal courts are independent, and are part of the judicial branch. But no, only the Supreme Court is part of the judicial branch, and they only review the tiniest sliver of cases appealed to them.
To restructure, I have thought in order to protect the people from the government, we need the federal courts to report to the judicial branch, the prosecutors report to the legislative branch, and the investigators remain within the executive. But this is so tremendously radical, and there would be large obstacles to accomplish this. So I would propose that a small percentage of prosecutors would be housed in your proposed OFOIS (Legislative branch) to pursue cases against Federal employees, and only the Federal Courts of Appeals be moved to the Judicial Branch. Cases against Federal employee would be initially tried in Federal Appeal Courts. Finally, Federal Appeals Court Judges need to be somewhat equally divide between former prosecutors and defense attorneys. Today most Federal Judges are former prosecutors, and they see things, judge things, and favor things like a prosecutor
Regarding Qualified Immunity, this term and concept originated from case law established by a 1967 Supreme Court decision. As such, is not the purview of legislative law making. Although try we might, it would probably be overturn in court. Here is a link to another post that explain in more detail. Police Officer Reform & Take away qualify immunity
Finally, are we, as a people, and as a government, trying to criminalize too many actions we deem inappropriate? I suggest we reduce-criminalize a number of our statues and make them misdemeanors and/or civil judgments with higher fines/penalties as appropriate.