Aha!
All this very long post to ask one more question: Are there fusion stones that have bonuses beyond level 1? How can one obtain them?
All NPC stones have level 1 stats. That's why the purified stones exist - they have no stats at all. So you can use them to transfer only the stats you want to transfer, or at the least control the transfer process better (using a variation of the following, with one of the stones being a pure one).
You can trick the NPC stones a bit, especially if you can get three with the exact same stats (or at least 2 matching stats). Use one to rip the stats you want off an item. If you have 2 items with the same high-level stat, use the second stone to rip the second one (or make it blank, like the following). Then use the third stone to rip no stats from a blank item, so you have only the base stats on it. That way there will only be 6 stats to transfer, and you're sure of getting the high-level one.
Or if you're flush with gold, and you could be at higher levels, you can see what's on the AH. I've found a lot of good fusion and mana stones on the AH, some cheaper than what the NPCs sell them for. I used strictly AH stones to tier two items up to level 4.