I think you're best to work to a "worst case" scinareo - assuming that you are getting the maximum expected level, in phase, into all your inputs at once. That way you can be sure that your mixer amp won't clip under any real-signal condition. You're right that just a single input will give a very low output (relative to all inputs driven), but that's just the same as the difference between playing one string and all of them at once. Don't worry about it!
Also remember that the guitar gives a very wide dynamic range output anyway, depending upon how its played, so your circuit will have that to deal with in any case. You may find that you wan to add a compressor at some stage, but they can be difficult to design.
Forgive me as I can't seem to see your attachements, but if the other guys think your basic design is sound then build it and just be prepared to adjust some resistor values to get an output level that works well in practice.