At this point I’d reconsider using a pre-made engine in the first place..
Viewing post in Inviting suggestions on engine options...
What do you mean? Start my own original engine? I would prefer to do exactly that, but that will take much more time than I have. If I could go back in time and tell myself to do that 15 years ago, then I'd be free by now and doing whatever I want. Now I have about four months left to try to salvage as best as I can. I can't develop a game that is it's own original engine in that time.
I don’t know what to tell you. You seem to be asking us to magically fix your mistakes.
In the time you’ve spent worrying about a correct/elegant codebase you could have already progressed a fair amount. Yes, modern engines suck, but then your only choice left is to not use one.
If you ask me, a good game must internally be what you call a clone generator, as it allows the engine to be specialized and optimized for that one purpose. Any changes can be done by changing the engine itself. This is best done by just making the game, without a pre-made engine.