Runes of Magic Advanced Transmuting Guide

First you should know there IS a priority list. and it DOES matter what slots items go in.

Here is the Priority list:
Original Item
Middle box
Upper Left box
Upper right box
Lower left box
Lower right box

Now for the stat priority:
Rank 1 attributes from the original item
Rank 1 attributes from the next priority box (ALL rank 1 attributes on that stone, if item is put into the middle box like I often do then it rips from the up left stone first)
Rank 1 attributes from the next priority box (upper right using item in middle)
Rank 1 attributes from next priority box(lower left using item in the middle)

NOW if you have not used up your 6 (yes 6) attribute slots. and when I say attribute I mean keyword str, brute etc. THEN it will do this:

Rank 2 Item attributes
Rank 2 next priority box attributes
Rank 2 next priority box attributes
Rank 2 next priority box attributes

IF STILL you haven't used up all 6 guess what it does .... Rank 3.

*Important side note: a yellow rank 1 mod is equal to a green rank 2 mod. i.e. if you have Brute 3 and the item has a Str 5 the Str 5 will be applies as Brute is equal to a rank 6. Max rank for a Green stat is 10 max rank for a yellow stat is 5. So you see the 2 to 1 rank ratio.

The ONLY way I can see to get a green "deleted" (which is really just dropped off) is to have it be a higher rank than the yellows you are putting on. (which currently is impossible)

As far as combonations go you can get 2/4 (which equals 2/8 when dealing with keywords) but more common is a 3/3 which is still good.

Also if you don't get what you wanted try reordering the stones according to the box priority (assuming you dont' have too many Rank 1 keywords)

I have given a video cam tutorial to a friend as well as explained this in game to several people who now understand it. However understanding and implementing are two different things.

Precision - Dex/Wis
Barbarian - Str/P.Atk
Keen - P.Atk/Def
Paladin - Str/M.Def
Defender - Str/Def
Mystic - Wis/M.Def
Fortify - Stm/Def
Warlock - M.Atk/M.Def
Fang - Dex/P.Atk
Reflex - Dex/Def
Agility - Dex/M.Def
Brute - Stm/P.Atk
Accuracty - Dex/Max HP
Illumine - Int/M.Atk
Savage - Str/Stm
Crystal - Max MP/Def
Force - Stm/Dex
Endurance - Stm/Max HP
Fox - Dex/Int
Genius - Int/Wisdom
Couger - Str/Dex
--------------
Soul - M.Atk/Wis
Sage - Max MP/Wis
Mind - Int/M.Def
Speed - Dex/Max MP
Resiliance - M.Def/Def
Savant -Max MP/M.Def
Monk - Stm/Wis

From what I have been able to gather all "yellow" keywords (those listed above) only go to a max rank of 5(or V) "Green" keywords can reach a max rank of 10 (seen IX so far) so just because it's yellow ... doesn't mean it's better.