"2. Even with the screwy fuel filters, we did manage to get the engine running. Now the major problem is that it starts at a high idle (around 2,000 rpms) and then quickly, very quickly, ramps up to its max. We can stop it with the fuel cutoff, but each time we restart it ramps up quicker. We aren't sure if this has anything to do with the new fuel filter setup, but we did have the older filter assembly off for a week and had to do some major bleeding and cranking to get the engine started."
Maybe your throttle cable or linkage is binding? Perhaps disconnect everything and see if the problem still exists. If so, probably something wrong with the high pressure pump / governor assembly. Sounds kind of scary, even though you can shut off the fuel you might see if there is any way to block off the air intake. Did the engine run properly before this? Any recent work done on it? Let us know what you find.