I made my own game, just like you're describing. Here's the Forum topic where I chronicled my progress:

https://pinside.com/pinball/forum/topic/flash-retheme-project

A few recommendations:

1. It helps if you're either an artist, an experienced programmer or an electrical engineer (or know people who are who can help). I'm an artist (the least valuable of the three) and taught myself the other two.

2. Think through everything before you start. Visualize how you want your game to flow, what you want each playfield element to do and how the modes will work (if you're going for mode-based play). Make sketches and diagrams. Do you want ball saves? Multiball? Mode stacking? Think through how different features will interact with each other before you begin. Your questions in the initial post show that you have a great start on this.

3. Don't give yourself a deadline. Take things one problem at a time and give them the necessary attention before moving on. Also, don't give yourself a firm budget. My build ended up costing less than a Ghostbusters Pro, but I'm still glad I didn't cut corners.

To make things way easier on myself, I started with a populated playfield and a used cabinet - it saved me about six months of build time and probably $1000. Because I wanted a completely new ruleset and sound package, I used P-ROC boards with an Asus Tinkerboard for a CPU and I did my programming in Mission Pinball Framework (MPF). Both P-ROC and MPF have excellent online forums to help with any questions you have along the way. My local library has a "maker space" with a laser cutter - I brought a sheet of plexiglass from Lowe's and a PDF file with my plastic shapes and 30 minutes later I had all my plastics. Graphics for the plastics, playfield, cabinet and backglass were made at a local sign shop - basically giant vinyl stickers.

Finally, be aware that once you start this project there will be times when you get frustrated and angry and want to give up. Just remind yourself that you're doing it for fun and focus on how awesome the finished product will be. You can do it!