Alan -
Good to hear that you're closer to a working setup.
If the pedalboard behaves well when it's in front of the F-1X but not in the effects loop, then this is probably an impedance problem with the last floor effect in the chain (your envelope filter). You could try removing it from the chain and see if the other stuff lives in the loop or not.
If this is a pedal problem, the way that you fix it is to put a buffer amp after it in the chain. This would be something like the simple amps that people use with piezo pickups - no EQ change and unity gain, but a high input impedance so your pedal will work right.
The Alembic stuff is designed to be simple and have wide bandwidth, which can lead to problems when you're in the area above and below what you can hear. If the SF-2 had frequency response out to 100KHz, there's no way you can hear it, but because it's not limited, you might be asking your power amp to amplify a highly boosted signal that your speakers can't reproduce. You can fix these problems with filters that get rid of ultrasonic frequencies. Alembic could have built these in, but I think they opted for purity and simplicity of the design knowing that few people would have feedback problems.
Ron's very sophisticated ELF-1 subwoofer controller was designed to optimize extreme low end response by creating an active boost that was very precisely tailored to the response of the speaker and cabinet. If I remember correctly, it had a settable subsonic filter that limited the bottom end response to save amps and speakers from extraneous subsonic stuff like handling noise. You guys may be too young to have played much vinyl, but back in the day of warped records and not much power, you could easily get weird periodic distortion effects when playing warped records with a good turntable.
David Fung