is one of Your 3 t12 build with yellow stats?
As the general theory says, every merge leaves only 6 lowest stats. But what if they have same rank? Here comes the trick.
Arcane transmutor cells have different priorities. Center is the highest, then top left, then top right. You don't need to remember this, just swap mana stones till you like the result.
There is one exception. Stats on items will have higher priority regardless of the slot (we are still stalking about same rank case).
This means you can make mana stones starting from low tier items and keeping your 6 yellow stats.
Basically, there are two options.
1. When producing t12 make sure one of them has the stats you want and then put it in the highest priority slot when tiering your weapon.
2. When you have t5 stone with 6 yellow stats make 2 more t5 mana stones (any would do) and apply your 6 yellow stats to the item. After this you can safely tier it with any 3 t12 stones.
Upd. One more detail. Don't use fusion stones you buy from NPC to extract yellow stats. If you do, you'll get a mana stone with both yellow and green stat of the same rank and they you cannot get rid of the green stat.
You can get fusion stones with level III and IV stats from public quests in Dalanis, Weeping Coast, Savage lands. If you use them with your yellow stat item, the produced mana stone will have only one level I stat, namely the yellow one and it can be safely merged with others.
Hope you don't mind the question, but where do I get the yellow stat items?
refer to http://www.rom-welten.de/en/content.php?inc=statrank to preserve yellow I's
you will need at least six fusion stones with green III's or IV's from the Dalanis public events
the yellow I stats come from blue items from starter zone mobs. high drop rate buffs helps. check AH
make sure to use only clean drops. not sure if drop rate influences clean item drops
here are the blues, yellow stats in ()'s and mobs to farm. sorry if the formatting is hard to follow.
Pioneer Trousers (Soul I) Fungus
Diter's Snow Coat (Speed I) Young Bear
Sentry's Chaincoat (Seclusion I) Wolf, Bubsitan, Cave Rock Scorpion
Blizzard Bow (Observance I) Wolf Cub, Bubsitan
Military Shield (Resilience I) Beetle, Northern Plunderer
Hammer of the Mother's Instructions (Oppression I) Wilt-leaf Bat
Nail Gun (Agility I) Kobold Miner
Vender's Lost Sword (Force I) Newt
Kobold Harvester (Observance I) Anglo
Long Cane Staff [green item always clean] (Genius I) Kobold Gatherer
Combat Robe (Savant I) Shadow Newt