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No, you didn't hurt anything.
There's no shutoff valve.
If you're draining the primary filter on the frame rail first, there's a chance it could siphon fuel from the tank.
I don't remember the exact procedure in the manual, but I think if you drained the two filters on the block first, left...
I haven't had to do any major work on my HH, so I don't know enough about the inner workings to be much help in that area. Hopefully someone with more experience with the HH will chime in on that.
A couple years ago I did the same thing you just did and replaced my HH O-rings because I was...
With the rubber covers bad, I'm not surprised there was crud in the threads. I doubt the lines or ports are clogged, but it's easy enough to find out. You can loosen the lines one at a time at the injector and start the engine and see if they spray diesel.
Also, look on the back side of the air filter housing toward the engine. There's probably a 1" port there that might have to be plugged, or else the board over the intake won't completely kill the engine.