There was (at least back then) an ongoing meta discussion about how to do better. So it might be useful to explore not just the organizational designs which were realized, but also the space of things considered. For instance, before Bush hit, there was discussion of tiny "fix that!" grants. Like there's one person who is an outlier in understanding how to do X, and their book just isn't getting finished. So rather than society waiting years on diffusion and reinvention (which is what ended up happening), it might be worth paying someone to sit outside their office, and stand on their desk, and be a forcing factor on making the book happen.
At least back then, with a failed attempt at a commerce ARPA clone, it was thought important to have a clear metric to prioritize projects. "What's better for DoD?", rather than the far less tractable "what's better for the commercial economy?".
Perhaps I missed it skimming, but a major issue has been the death valley between research and commercial impact. And attempts to address that making things even worse (ie, researchers encouraged to think commercialization, sacrifice impact by holding things close, and then commercialization generally fails, so there's no offsetting benefit). And there's the unfortunate pipeline from research to patent to unsuccessful startup to dominant company having yet more anticompetitive ammo. I wonder if it might be fruitful to broaden focus to the research pipeline rooted in ARPA? Because a successful clone would presumably again face this difficulty. And there might be some other design point that is less ARPA-like, but does impact better.
How well ARPA works comes and goes. It's not a stable equilibrium. So instead of asking how to create a successful clone, perhaps one might ask how to create something viable in the vicinity of success, and separately, how to increase time spent less distant from success?
The difference between an old-school autonomous PM, rolodex and checkbook in hand, showing up on your doorstep and saying "I've heard you interested in doing X - what would you need?", and say NSF exploratory grants of "groups with the following characteristics, may submit grants addressing the following issues, with a deadline of mumble, and the following logistics"... is really really big.