Hello, I assume by your username that you're the author!
Transpiling is normally a little risky. Transpiling with a custom transpiler over ~500KLOC is downright terrifying.
I'd be concerned that the cure is worse than the disease.
I understand the allure of this solution. Bringing 30ish years of code into the modern era with a single piece of code sounds like a huge win. But you owe it to your employer (who seems really gracious and trusting) to ask:
1. Are there edge cases? Programmers are a clever bunch, and you can never be too sure about what features/bugs they've used/abused!
2. How will success of the transpile be determined? I'd use unit tests, but that'd take a lot of unit tests!
3. What % of that code path is critical? Can you get away with ensuring the functionality of a subset of the codebase? If so, could you just manually port that?
4. "Blaming the compiler" will be a reasonable excuse for any problem over the next year or two after deployment. I guarantee you'll be spending time proving that other peoples' mistakes are not your fault. How much flak are you and your boss going to take for this?
5. Since the code can be linked, might a more popular language (that will be known by a wider community) with a slow porting plan be reasonable?
6. Python is commonly used with scientific computing. Why does this case preclude it? If you are doing mostly numeric processing, that gets directly passed to the hardware anyway!
You have been given a rare chance to pay down technical debt. From what I understand of your solution, I believe the bespoke transpiler and semi-known language will ultimately increase it. And I know you love D, but if I were brought in as a consultant, I'd be recommending the .dll/.so solution with Python. If something is really time sensitive, use Python binding to work with other languages (avoiding premature optimization).
Even if myself or my fellow posters made a point that resonated, it might be too late for such discussions. I can't weigh the political costs for changing strategy now. So I'll wish you good luck, and hope that Extended Python doesn't have too many sharp edges for you to contend with. I hope to see a postmortem a few years from now detailing the outcome of this plan.