Hi Brian, I hope you’re doing great :-). Issues could be present as each time you run the Makefile, git makes changes locally. To make sure the build.sh file is getting modified, you should check the ~/PYNQ/sdbuild/build/ directory and search for the build.sh copied there. Lines after the 105 are not needed (since they are forcing the Pynq repo to be cloned again for the Pynq-Z2 and compile the original overlays). One workaround could be to just delete those lines by hand.
I’m sorry I can’t guarantee the Makefile given will work as it is, because among tests I loss track of the changes made to my local copy of the PYNQ repository 
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However, I’m sure you could get it working following the aforementioned 
Please, let me know as soon as you get it.
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