A couple of InDesign features which may help if you didn't already know…
The Book feature allows multiple InDesign files to be combined. You could put all of the shared content in one InDesign file and all of the neighbourhood specific content in their own respective InDesign files. A Book could be created for each neighbourhood which combines the relevant files and from this a PDF can be exported.
Window > Type & Tables > Conditional Text
The Conditional Text panel allows for the showing and hiding of different pieces of text within the same document. This could be a good option if the difference between your unique publications is relatively small. The conditional text section on the following page is quite comprehensive...
"I'm trying to decide if this is the best way because I'm having some problems."
If you can explain the details of the problems, it will be easier to help you decide whether a different overall approach would be better, or perhaps only a small workflow adjustment is needed.
As an experienced newspaper production pro and consultant for developing and refining production systems for other publishers, I strongly recommend against using layers to generate your replates for each edition. You want to be generating unique InDesign document files for each edition replate to ensure that you're putting the right content on the right pages for the right editions. Your current workflow is fraught with peril. Full stop.
You need to build a master template with the common elements pre-loaded with master pages that contain the elements you use for every issue (nameplates/mastheads, folio lines, stock art/fillers, house ads, etc.), which is then used to create an issue master template which contains any common elements (common display advertising running inside your replate for that issue, refer/inside boxes for common pages inside each issue edition, etc.) to build a unique InDesign document for each edition replate, for each issue. And you need to be saving separate InDesign document files for each edition replate, for each issue.
I can easily imagine the problems you're having trying to use layers in a single file to generate your edition replates on the fly. With one file, which is constantly modified on deadline, you have no quality controls to ensure that you're putting the right content in the right edition, and no version controls to sleuth where problems are occurring and what needs to be done to fix them. All you can do is start over on the edition from scratch to fix the replate when problems happen, in the worst-case scenario after the press crew starts clicking off copies from the press. I have no doubt that your current workflow is putting you and your publications in a World of Hurt.
If you need help with this, feel free to contact me through this forum by responding to this post or by message. There are a lot of sharp folks here who can help you. I'm just one of 'em. But if you need help to work your way past these issues, I'm happy to lend a hand.