Russ, I took a quick look at your repo. It's a bit confusing, as there are two different WinAGI project folders, one in bins, and one in ltec-gds. It looks like the one in bins was your first try, as it's older - the other I see you were working on it last night.
I'm not sure exactly what trouble you're having. I checked, and WinAGI shouldn't throw disk/file related errors when deleting existing resources. What I suspect is that when you deleted them, logics that reference them will throw a compile error if you try compiling the game. All of the resources in the template game are used somewhere in the game, so if you delete one or more of them, you will also need to edit the logics where they are referenced.
For what you want to do (create a new game based on your existing resources), the best path would be to create a new blank game. Then import all your resources (I'm sorry I don't have a bulk import function - maybe that's something I need to add in a later version). If your logics are fully compatible with original Sierra, they should then compile with no errors. But I suspect there will be a bit of tweaking required to iron everything out. WinAGI will help you with that- if you try to compile a logic (or the whole game, which automatically recompiles all the logics), it will identify errors (displayed in red and indicate that the logic can't be compiled until you fix the condition) or warnings, which offer helpful advice on how to improve your code or avoid game runtime errors. You can ignore the warnings if you want - you don't have to deal with them to compile and run your game.
I did notice that in your first try (the files in the bins folder), you had your defines file listed as logic zero. That would indeed cause a problem. Logic zero MUST be the main logic - the one that runs every cycle and never gets unloaded. It looks like you got that straightened out when you tried using the template.
It also looks like you figured out how to use the global defines file. That makes it very easy to manage defines that are used across multiple logics. Here's a tip for you - you don't need to include defines for logic, view, picture, sound resources; their IDs are considered global defines by default. So if you've given your resources IDs that match what's in your globals.txt file, you can remove all those defines from the file.
There is a ton of helpful information in the Help file that should show you how to do all the things you need to finish adding all your resources and getting things running. And you can also always contact me, either here in the forum, or by PM, and I'd be happy to answer any questions you have - either about how to use WinAGI to do what you want, or generic AGI related questions.