Sounds cool. Generally, what would you borrow from each one?
Without going all the way into my Realm of Stars RPG I've been building that's become its own classless 3.x beast, if I were to run 3.x again:
1. 3.0's Combat Chapter.
2. 3.0's DMG.
3.
Probably the 3.0 MM + Monsters of Faerun as my base. Maybe I use the 3.5 Update booklet to revise their DR, but I would want to keep the noncombat stuff 3.5 cut out. Spells: 3.0 version's of Bull's Strength, etc, and 3.0 Darkness. The 3.0 "Animal Friendship" (I think that's it's name) would be available as well.
4. 3.5's PHB's Feats; Equipment; Races; Skills, and DMG Magic Item Pricing Formula. 3.5 version of most spells. If they're like Bull's Strength though, where their durations were drastically reduced, I probably roll back to the 3.0 version.
5. UA Test-Based Prerequisites.
6. PF1's Spellcasting Concentration check difficulties.
7. PF1's Spell Design framework from Ultimate Magic.
8. The Wound Thresholds and Background Skills from PF1 Ultimate Campaign (I got Background Skills from Shadowrun 4e first, but PF1's version is similar).
9. I'd start from some PF1 versions of the PHB 3.0/3.5 base classes, plus the Magus (Which is basically Arcane Archer + Eldritch Knight as a base-class). (Swap fighter for Slayer; Monk would either be the UA version or pre-emptively archetyped (if kept - I could see an argument for remaking it as a variant of Ranger), plus the PF1 Dreamscarred Press Psionics if I do Psionics. I would do a curated sublist of decent archetypes).
10. PF1 Core's Favoured Classes. Extra skill rank or extra hit point.
11. 1 for 1 skill point
costs (like PF1); but Cross-Class skills keep the lower cap they have in 3e.
11. Use the revised Level Adjustments from Giant in the Playground + Oslecamo's Monster Classes for less crappy playable monsters.
12. Probably use some manner of innate enhancement system to replace Wealth By Level, just for simplicity. I like not having to worry about people arguing over loot or wealth distribution, and not wasting so many whole sessions shopping, etc. Magic items would exist, but they would replace your plain enhancements. If you're not going to build a better one custom, there's one in Pathfinder Unchained you could use. Or Trailblazer. And then you give out ~1/4 the treasure and you don't need to worry about wealth imbalances so much.
12. Justin Alexander's Diplomacy rewrite.
13. Trailblazer's iterative attacks.
14. If I use PF1 monsters or the Candlekeep Realms Bestiaries or EN Creature Catalogue to expand beyond the base (I probably would) I would try to give them appropriate additional noncombat stuff like the 3.0 monsters if they lack it.
15. Extra Gear from PF1 Ultimate Equipment, and 3e Arms and Equipment guide, and the version of Incantations found in Kobold's Deep Magic for PF1.
16. Then I would step through my 3.0 and 3.5 FR content and see what doesn't make the cut, that's most of my expansion content for players.
That's more-or-less the basics of what I would start with before I start more seriously reworking things.
What are the most essential things I would rework personally rather than grabbing an existing rework?
1. Flatten and simplify feat prereqs so they're not such a pain to plan for.
2. Pick selective 2e-inspired nerfs to spellcasting from the 3.Y houserules document. For starters, Go back to 10 min/Lv Spell prep. Wands will need to get more expensive. Potions may still be fine.
3. No divine "you know the whole ever-expanding-spell-list". Divine casters have spellbooks.
3. Sorcerer and Bard will need their spellcasting revised if they're to be included (I cut them entirely from RoS and went down to three spell-lists).
Unsurprisingly, this frankensteined 3.x I put together was my starting point for my system-in-development, but at this point many many things have been rewritten from there (like how it's a classless point-buy system now), and it's tailored to my setting. Still. If I were to run D&D-branded fantasy game again, it would be the heavily modified 3.x hybrid described above, not "everything 3e" or "everything 3.5" or "everything PF1".
[Note: I may have forgotten to note down a handful of things, I didn't consult any notes to write this, it was from memory.]