Re: Merging Harmony Demos for Specific Application [Without BSP]:
1) Recommend you create fresh project, no BSP, pins defined in pin manager, modules & clocks set in MHC. Then generate, and appropriately copy code from sample projects (or even better copy code from examples created using MHC-App-Generate).
You can modify the generated .c and .h files in your project folder, but avoid modifying other files types (instead change MHC so files generated properly).
Avoid modifying library files, better to copy them into your own custom folder, and set the paths in project settings to find your folder first, or even better rename the modified files. This will make it safer should you later upgrade Harmony version.
Keep a good list of everything you modified, again so you have it for another harmony version, or for another project with similar needs. Especially true for patches and bug fixes.
2) Yes, as per (1)
3) Avoid BSP. Those are a carry over from Harmony 1.0 and are totally unnecessary in Harmony 2.0. Instead use MHC settings like Pin Manager.
4) No, start with a fresh project. Copy in only what you need from other projects and examples. Many were created by different people with different styles, and some have "leftover" MHC settings. Take the time to go through all MHC settings and make them your own. Using an old project I've found you can't fully undo things added by MHC, so start fresh, backup/commit often, that way you can go back to "before" and cleanly fully remove something not properly added.
Do the "merge" manually so you know what is done. Same for harmony upgrades. Hopefully when upgrade the list of "patches" gets shorter, but sometimes you have to add new ones :/
(Shortcuts are things well proven by grandparents, any newer shortcuts should be temporary or you'll end up paying for them later).