Thanks for your interest in Hall of fame and MapFinder, answers in red below.
1. Can I make multiple 4000BC saves like in the manner I outlined above? Yes
2. On t0, can I move warrior before making a save? You can, all you need is a t0 save.
3. Could I settle before making a save? You can, all you need is a t0 save
Note - once you have taken an action you can't go back and replay the game and choose a different action.
4. Is the saving method in mapfinder (pressing *rename* and *move* file) necessary for validation somehow? No, it is there for your convenience only.
5. Is there any way to "save" or default the custom game setup, so I don't have to spend a couple minutes repicking civs/settings after playing a game? Yes, once you have the game set up before running MapFinder manually create a save and name it accordingly e.g. NobleStdRomeTemplate.
6. My mapfinder/game tends to crap out around ~2000 searches and 1-2 hours. Ideally it would run my entire workday. What map finder search settings work best for this / or any other tips on boosting performance? I regularly run MF overnight generating thousands of maps with complex rule sets and have never seen this, modern PCs should be able to handle MF and Civ IV no problem. How much RAM do you have?
>>I'm not sure autosaves are generated when I'm essentially opening a 4000BC save (say the next day), moving to see if it's going to be viable, and then saving it to play a future day. You don't need an autosave in that circumstance as you have the 4000BC save, just make sure you play from your manual save the next time.
>>Basically, sift through MF for 100 maps. Copy all those at once from the mapfinder save file to a secondary folder. Open up those maps, to filter it down to ~5 saves that. Rename/resave those into my primary folder. Possibly might even do this filtering multiple times (first to sift through total land count, next to sift through viable resource configurations). Nothing wrong with doing that, just make sure you don't end up accidently playing from the 4000BC save, make sure you're playing from the latest one. If you are interested in land count one tip is if you look in Windows explorer and filter for the saves yourself you can see which files are bigger or smaller than the others which may be an approximation for what you want.