So I want to have 2 Augusteses (Augusti?) running in parallel, one in Digital Mode onto which I can record riffs and basslines, synchronized to the host, and the other for freeform tape-loop ambience to layer on top. The same audio would provide input for both instances.

For example, I would record a clean guitar part and maybe a synth bassline on the Digital Mode instance, set Feedback to 100%, and then play with the tape-style delays on the other instance. What would be the least painful way to facilitate this? I can't set either to receive MIDI from all channels, because I'm controlling soft synths and effects on other channels and don't want to pitch-shift the loop etc. when I'm sending CCs to another plugin.

There doesn't seem to be any way to toggle input mute in Reaper, but I have been working in Bidule lately so maybe someone could suggest something? I just need a way to hit a key on my laptop or send a message from my MIDI pedal that "closes" one instance of AL.

You could use a MIDI script so that Augustus only responds to the CCs you're interested in sending it, and then make sure they don't overlap with other plug-ins etc.

Or you could use MIDI routing/filtering in your DAW or something like MIDIPipe.

In Bidule, I found a way to use some of the built-in routing tools to allow selectable switching of audio/midi signals from one path to another. Now I just need to find out if those switchers are THEMSELVES controllable by midi or keyboard commands...