It's so long since I had an FX loop or a posh pedal like the Modfactor I may be talking cr@p.
Assuming the Egnator is line level Loop out then in on the Modfactor should be line but out should be AMP as you're feeding another pedal which is expecting an instrument level signal, maybe, I'm in over my head, but instinct tells me that that is how to set it.
The Egnator FX loop is buffered anyway so maybe leaving that off in the Modfactor is correct.
I'm afraid that's as far as I can go, I should never reply in the Tech section :D