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@Barnes_Law your article of June 11, 2017 lawandcrime.com/high-profile/s… on Mueller-Comey conflict was prescient. According to Mueller, Trump tried to persuade his lawyers, Special Counsel Office and DOJ that this was disqualifying conflict (as you had argued)
2/ in Mueller Report, Trump's attempts to get swamp to take Mueller's conflict of interest seriously were portrayed as obstruction of justice.
3/ Mueller reports that, on June 13, 2016 (two days after your article, which was clearest of contemporary article, but there were others), Trump's lawyers sent letter to Special Counsel Office, complaining about conflicts, including Mueller's "personal relationship with Comey". 
4/ next day, June 14, a bombshell story was leaked to WaPo by Mueller team (or sympathizer in admin) that Trump was under investigation for obstruction. Leak was perhaps in retaliation for complaint about conflicts or perhaps mere malice.
5/ this very damaging leak prompted Trump to call McGahn to bitterly complain about Mueller's conflict of interests. These calls are described in Mueller Report. Trump wanted McGahn to do something about the conflicts. McGahn didn't want to touch Mueller conflicts with bargepole
6/ on June 15, according to Mueller Report, SCO informed DOJ of concerns communicated to them (which ought to have included the issue of Mueller-Comey friendship as conflict for obstruction investigation) and told Trump's counsel that DOJ "could take any appropriate action"
7/ Mueller Report citation for their communication to DOJ is not shown as written document, but merely their notes. It appears that this important conflict issue was handled by a telephone call and then dropped by both Special Counsel Office and DOJ
8/ 28 CFR 45.2 law.cornell.edu/cfr/text/28/45…: Mueller cannot participate if he has "personal" relationship with "any person [Comey] ...which he knows has a specific and substantial interest that would be directly affected by the outcome of the investigation..."
9/ confronted with this conflict of interest, Mueller was obligated under 28 CFR 45.2(b) to "report the matter and all attendant facts and circumstances to his supervisor". The telephone call from SCO on June 15, 2017 clearly did not constitute the report required under 45.2(b)
10/ had Rosenstein been properly informed, he would be obliged to relieve Mueller unless he issued determination "in writing" that Mueller's participation would not create "appearance of conflict of interest likely to affect public perception of integrity of investigation"
11/ obviously none of this happened. It would have been impossible for Rosenstein to determine that Mueller's participation would not impact "public perception of the integrity" since it was already a huge public issue in June 2017
12/ neither Mueller nor Rosenstein complied with 28 CFR 45.2 in relation to Mueller-Comey personal relationship (bromance).
13/ Handling of incident in Mueller Report is order of magnitude worse. Mueller Report not only ignored breach of regulation by Mueller (and Rosenstein), but portrayed Trump's effort to require that they observe conflict regulation as obstruction of justice.
14/ both Mueller Report itself, and, especially, Mueller's bizarre press appearance show that Trump was entirely in the right to have been concerned about Mueller's lack of impartiality in regard to Comey and obstruction.
15/ Mueller should have immediately recused himself from the obstruction investigation. Alternatively, he should have fully informed Rosenstein of conflict from his personal relationship with Comey according to regulations, with Rosenstein then relieving him of obstruction case.
16/ reader NelliesHamRadio drew my attention to important Dec 2017 story on Mueller ethics waiver politico.com/story/2017/12/…, describing response to their FOI request.
17/ DOJ produced one-sentence waiver for Mueller under 5 CFR 2635.502(d) dated May 18. They refused to produce a two-page recommendation but refused to produce it on grounds that it "would interfere with deliberative process inside the department." Should be easy to declassify.
18/ from this FOI information, one can deduce that DOJ ignored request from Trump's lawyer that they consider conflict arising from Mueller-Comey bromance, not even giving them a written response. (Failure of Mueller Report to cite such a document further supports this view.)
19/ no evidence that DOJ had been informed of or considered Mueller-Comey friendship/bromance in their May 18, 2016 opinion. Nor is there any reason to believe that they were concerned about anything other than Russian collusion, where personal relationship much less relevant
20/ also interesting that they issued opinion under 5 CR 2635.502(d), but not 28 CFR 45.2 discussed above.
21/ one's first instinct might be to say that it doesn't really matter whether opinion was issued under 5 CR 2635.502(d), as opposed to 28 CFR 45.2(b), but Mueller charged Flynn (who, with legal advice, registered under another lobbying program) for failing to register under FARA
22/ 28 CFR 45.2 law.cornell.edu/cfr/text/28/45… is part of the code for Department of Justice employees, while 5 CR 2635.502(d) law.cornell.edu/cfr/text/5/263… is less specific code for government employees.
23/ 5 CFR 3801.101 law.cornell.edu/cfr/text/5/380… specifically states that DOJ employees are additionally "subject to the conduct regulations contained in part 735 of this title AND 28 CFR part 45". Respective regulations therefore have to be checked for differences.
24/ watch the differences between the two certificates. 5 CFR 2635.502 triggered under NARROWER criteria: requires "direct and predictable effect on financial interest of member of household" or "person with whom he has a covered relationship" AND reason to question impartiality
25/ by definition, a "covered relationship" is a "business, contractual or other financial relationship" - which didnt apply to Mueller-Comey relationship.
26/ in other words, Comey-Mueller relationship doesn't meet criteria of 5 CFR 2635.502.
27/ however, this is not the case for 48 CFR 45.2 (which I'll get to in a couple of hours from now)
28/ 48 CFR 45.2 definition of conflict for employee participating in criminal investigation much broader. It includes "any person... substantially involved in the conduct that is subject of investigation". 48 CFR "personal relationship" also broader than 5 CFR which was limited
29/ to financial interests and/or "covered" relationship.
30/ bottom line: Mueller-Comey personal relationship fell well within 45 CFR 45.2 disqualification for DOJ employees participating in criminal investigation, even though it did not require disqualification under 5 CFR 2635.502 (ordinary government administrative employees)
31/ bottom line 2: Mueller did NOT obtain correct waivers from DOJ. He needed certificate under 45 CFR 45.2 in addition to waiver under 5 CFR 2635.502. However, DOJ could not have honestly granted 45 CFR 45.2 waiver.
