This is for everyone in this Q/A forum. I am having the same issues and finally decided to just try another DAW. Cubase was abnoxious so I figured that GarageBand might work better and it is compatible with Logic. Worked great for me. I recorded my tracks directly into GarageBand and now here is the trick after you get it in there:
1: Plug in the Zoom (USB). Open GarageBand, create a new session "Instruments", and then create 8 tracks.
2: In the Track info pane, assign each real instrument track to a different input channel accordingly (Track 1, 2, etc...) You should see "Stereo 1/2 input microphone" already selcted and will need to change that to a mono track 1, 2, 3 and so forth.
3: Go to Preferences, Audio/MIDI, and make sure your input/output reflect "Zoom R 16".
4: In Preferences go to "Advanced" setting and make sure the following are selected: Real Tracks (8), "Automatic" for the next 2 dropdowns, "Auto Normalize" is checked, and under Audio Resolution "Better" is selected.
5: Record enable all your tracks and begin recording - making sure there is no clipping of course.
6: Once you are done save your session where you can easily find it, desktop worked for me, and close GarageBand.
7: Open up Logic, empty session.
8: Under file select "Open"
9: Find your GarageBand session you saved earlier and open it.
10: You'll see the name of the project already provided, make sure you check the "Copy external audio files to project folder" and "Copy EXS instruments to project folder", then select "Save". The newly created session should have all 8 of your audio files and now you can plug and play with them in logic.
I know it's a pain, but at least you can get a recording down and use Logic for your mixing. Just a heads up though, I'm using Logic 9 and I haven't updated GarageBand since last month or so, but it's worth a try until Zoom gets things figured out.
Let me know if it works out.
-Peace