1. for higher rarity items, it is more cost effective to merge them first then temper.
2. There are 2 ways to get duplicate monsters, first with a Nest in the village the monsters can appear twice during starting team selection. The other harder way is go to nests during the run, use egg sense to get a specific monster thats not on your team but do not hatch the egg. Since it is still not on your team, you can keep repeating this at more nests until you have as many duplicates as you want. Then hatch all of the eggs.
3. Save scumming is up to personal preference. I intentionally didnt try to limit it that much because ultimately its a little single player game for fun, so if thats something you want to do go for it!
4. 6 loops is pretty good for endless! Beyond that youll want to start seeking out the really strong combos (whether its items, synergies or mosnters). Consider selling food such as Calcarrots if your team's main strat isnt Int based. Also Forge Sparks from the Desolate Forge event are pretty important for really broken builds.
I'm glad youre enjoying it, sorry for the late response