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Of the default factions he'd be with the Minutemen, as boring as that sounds. However, the BoS is a possability due to his militaristic nature and the order they will instill (for some that order will be enforced at gunpoint of course, but the punisher has no problems with that).
Considering Shaun wouldn't be Shaun anymore, he'd probably put him down, possibly be on his own or join The Minutemen or work with The Brotherhood of Steel.
He'd likely shoot Father, Ayo, whoever drafted the plan to replace Roger Warwick, and all of the Coursers before giving the rest of the Institute leadership a very stern warning that he won't be so nice the next time, then tell the BoS that the situation is resolved and they can stand down; if Maxson refuses to see reason then it won't end wall for most of the BoS as well.
To that end, he might briefly ally with a group like the Minutemen or the Brotherhood, but only so far as it would further his own goals. Of course, his methedology would probably be far too brutal for the Minutemen (torture, rampant slaughter of "the enemy" with no quarter offered) in the long run, but they'd be a decent fit in the short term. The real problem would be that Frank is far more interested in obliterating the "enemy", and almost entirely uninterested in building or maintaining settlements (outside of killing the people who might threaten them).
Likewise, a long-term relationship with the Brotherhood would probably be impossible, because he simply wouldn't care about their ideals when it comes to capturing and preserving technology. He would only remain with them for as long as they showed willingness to assist in achieving his own goals, and he moment they balked he would leave. If they tried to stop him, then violence would almost certainly ensue.
He would likely see the Railroad as a waste of time, treating them in much the same way as he would treat any of the hundreds of naive super-heroes that he's had to deal with in the comics.
He would absolutely kill Shaun and wipe out the majority of the Institute, given the crimes that they've commited against both him and the Commonwealth.