The guitars have two outputs. I want to be able to switch between one signal or the other instantly (this can be done already just by changing rig in a performance) as well as being able to blend the two signals to have acoustic attack mixed in with electric. However, blending from a single output/input means both signals go through both the Stack and Parallel path . I want the ability to separate these but still have more than 1 FX on the parallel path.
I have a similar guitar, Tom Anderson Crowdster Plus 2. I have found a way to handle what you are talking about on the Kemper that works for me, maybe you can get a bit of inspiration from it. I run the electric signal to the input as normal, effects and amp as expected. For the acoustic signal, I use a separate unit to treat the acoustic signal, send it out in stereo to the “AUX inputs” on the back of the kemper (the same inputs you would use to monitor an MP3 for example). In my case I use a Boss AD-10 which has 1/4” stereo outs. I then turn the aux signal up on my master output. In this way I use the kemper like a mixer to balance the electric and acoustic signals at the kemper then send one stereo signal to FOH, then I can do what you want which is playing acoustic and electric at the same time.
I do understand what you are saying, you want to be able to plug in your untreated acoustic signal directly into a 2nd kemper to treat your acoustic signal in the parallel path, but not have it treated the same as your electric signal. Because what you are wanting is not possible, the above is the solution I have come up with that works for me.