Appeal to authority:
I have flown numerous Angel Flights to Logan
I have hit jet wake once in my career, squarely, violently, on short final to 4R at Logan.
I have had a vacuum pump failure in IMC.
His radio behavior wasn't as crisp as you shoot for, but had he landed and flown for another 20 years, it would have seemed nothing out of the ordinary (except, at the end, when he more or less wasn't responding to calls from the controller, answering a low altitude alert with his heading, apparently). I've heard much worse, even in IMC at big airports like Logan (um, er, say again...) and no one crashed.
A wake turbulence encounter of any significance would have killed the flight immediately. It is difficult to overstate the violence of a jet wake encounter. IMC at 3000? You would be a lawn dart. There would have been no leveling off at 1200, and no further radio calls.
My guess? He had a medical emergency. A stroke, a heart attack, a fainting spell. It would explain the behavior of the aircraft. He passes out, the plane starts a descent. He regains conscious control briefly, realizes he was low, mis heard the controller's low altitude alert (he had flown through the localizer, I could see the confusion over what the controller was asking for). He started a climb, stated his heading, had another medical event, that was that, plane entered a final spin.
My wake encounter was on a clear sunny day, maybe 300 feet above 4R, with jet traffic departing to the east underneath me (11?). Flew through a big jets wake (an A340 I think) at a right angle. My plane rose and fell 6 feet faster than you could comprehend the event. Had I been lined up with the departing traffic, there is absolutely no doubt in my mind that that would have been it. The overwhelming power of the event was incredible (in the true meaning of that word). Landed uneventfully, mechanic never found anything wrong with my plane. Ground crew at Logan saw it and asked me about it, my comment was "holy sh*t". I have 2100 hours, lots in bad weather and I have never hit turbulence even remotely approaching it. Maybe flying directly into a tornado would match it.
Yeah, yeah, I'll just roll my plane through it, you think. Um no. And in IMC at 3000? You wouldn't even know what happened. Lawn dart. On the scope one second, gone the next. So no, he didn't hit wake turbulence. If the angel flight pilot had a jet wake encounter in IMC, and regained control while still in IMC while losing only 1800 feet, then he was a fantastic pilot. In which case, it makes no sense that he couldn't finish the flight. He had a medical emergency.
As far as Angel Flight having three accidents after many years of having none? Random doesn't mean even, it means random. Be another 20 years before they have another.