However, I propose a somewhat different approach to Proto-Traveller: Box-Centric Traveller. Inspired by Tales to Astound's highly recommended Traveller: Out of the Box series of blog posts, this focuses on the first three books, included in the original 1977 boxed set, admiring the sound design of that original edition.
However, As opposed to "Strict Proto-Traveller", in which one uses these three books exclusively, Box-Centric Traveller permits material from later books, provided that it does not contradict the 3 Books, and provided that this later material is carefully chosen to preserve the original spirit. This means, for example, that one should be extremely careful when using material from Book 4: Mercenary, but should not ban it outright, especially as the rules for hand grenades are first presented in it, and as some weapons in that book would be conductive specifically to military-themed Proto-Traveller games. On the other hand, the Advanced Character Generation System is definitely out, especially due to the vast number of skills it grants characters, and big guns such as VRF Gauss Guns and FGMPs are carefully considered or even relegated to "McGuffin" status.
This also means being careful with S4: Citizens of the Imperium. While its rules on archery are invaluable, and while some of its careers are beneficial to a Proto-Traveller game, other careers are problematic, include narrow Book 4/Book 5 skills, or grant starships too easily and without enough strings attached. Everything outside the Three Little Books, as you see, is considered on a case-by case basis, to avoid breaking the spirit of the first three books.
For example, one may want clear rules for shipyard capacity (i.e., how many ships the shipyard can build at once). It is always possible, of course, to make them on the spot, but A5: Trillion Credits Squadron already has rules for it. Does that mean that other A5 rules, such as using High Guard ship designs, must be included as well? Of course not! But Box-Centric worldbuilding will greatly benefit from such rules.
The key here is treating the Original Box as the core rules, and avoiding contradicting it or its spirit, rather than adhering to specific publications. This means, inter alia, a small-ship universe using Book 2's drive TLs and no empty-hex jumps; a weaker interstellar government rather than the all-powerful Imperium of later Traveller publications; a focus on high adventure on player character scale; using Book 3 world distribution, with high-tech, high-population, Starport A worlds being rare; and keeping modifiers to the 2d6 curve limited to avoid overloading it.
This is my proposal for one way to play Proto-Traveller.