01) His office building was destroyed with military-grade explosives. They may even be able to determine that they came from/around his office.
This really should cause them to want to question him. Not necessarily arrest, but at least question; especially how high profile it was. Unless, of course, in the last year they've already found a patsy and blamed it on him.
02) His destroyed car was presumably found outside the broken-and-entered home of the local cop investigating him.
I think the nature of the two-cars merging and the destruction at Rudolph's place may be so odd that reasonable explanation will be futile. Thus we can expect a "gas main explosion" from the house hurdling one car into the other type story rather than actual arrests.
03) His house was burned down while he was there, and it started at the entrance to his sub-basement apartment.
Yes, but the heroic nature of his activities afterward, and witness testimony pretty much covers him there. After all, a KotC can testify on his behalf, and even if people don't believe in them, they somehow always seem to be taken as honest.
04) Witnesses will place him at, and fleeing from, the FBI building while it was under attack from 'South American Drug Cartel Assassins'.
Actually, no, he left through the NN. No one ever saw him leave the building; and an FBI agent is probably prepared to vouch for him, so I suspect he is safe on this one.
05) He was known to be at a houseboat not registered to him, where enough blood was found to indicate a murder took place. But not his, seeing as he's alive.
I think they have enough eyewitness (or close enough)accounts to stand up to his argument that he was just injured and survived. After all, Murph was ready to believe that. And the boat owner isn't pressing charges or making waves...
09) He may be tied to any investigation involving Molly, if she has been seen and recognized while masquerading as the Rag Lady.
Not more than her parent's say, as a known associate, not as someone accused of anything. Plus, with Molly and Lea's illusion ability, it would be easy to have the rag lady appear dramatically different at different times, thus easily making identification impossible.
12) Further investigation may reveal that his destroyed home has been bought and rebuilt into a small fortress by a known gangster.
Ya, but that's just weird; not a crime.
13) Further investigation may also place the former cop at the building, and associating with criminals and mercenaries at that location.
But not at all related to him.
14) Most importantly, he has civil charges still levied against him on behalf of Larry Fowler.
True, but he's had those for years, and the rest are all old news.