I often run R05>CA Ugly (preamp) > CAFS, so a similar setup. That said, I always run it into my Line In jack, not my mic jack. You mention loud and acoustic. In my experience, Acoustic is rarely loud, when looking at the ability of these types of recorders especially when compared to other types of music. Did you have Plug in power off? Where were your meters? They must have been barely moving if you had that quiet of a recording. What were your switches on the back of the deck set at, primarily gain. It is difficult to say without knowing all your settings, because those could affect the outcome. I know that if I am recording an acoustic show through line in, my gain is on low (sometimes I could raise it to high, but I don't) and my levels could be anywhere from 45 to 80 depending on the volume. I keep the low cut and limiter switch off. My CA Ugly is the original type, so there is no gain switch on that, it remains constant.
More information could help, I will confess though that having never used the mic input, I would guess that would be more sensitive, but again without knowing your settings, it is tough to say.