506,
I used to try and have everything always live on dedicated channels with several interfaces, but ran into similar issues a few years back. I have now simplified down to a 'staged' approach.
I have an in-rack mixer (Behringer pro 8 channel) and patch panel Behringer 24x2 with per channel half/full/thru normalling) that allows me to swap instruments in and out easily (using half-normals on the patch panel) with my 'main' setup always patched through. I use my Saffire Pro 40 for the main stuff, but it's back panel is also brought out to a front panel that I made up. I also have 8 ADAT channels (in an actual ADAT that I only use the A/D converters) running into the ADAT input on the saffire for extra channels. My Mackie mixer feeds those. For MIDI, I use a single channel and I'm just anal about using the sub-channels...I typically have 4 of 5 MIDI input devices, but they are all coded to a unique channel and I just connect them in/out/thru. That way, I can have up to 16 soft-synths...each on unique channels.
With this setup and ASIO driver I can run a lot of stuff...a couple of synths, bass player, a miked drum kit, several vocals, a saxophone, etc...and track live. Then I can singletrack over the live recordings in the polish mode.
Not trying to start a fight...just putting a thought out there...