Will we ever be able to get a T9 or T10 mana Stone from our item that is T9 ot T10 currently if we try to combine a puri and a T8 lvl 60 Purple we get a T4. We should get atleast a T7 from a T9 and a T8 from a T10 if not an equal stone.
What you are implying is that the process of transmuting the piece of gear with a puri should produce mana stone of the tier that has some relation to the current tier of the item. Currently it is only based on the natural tier of the gear, so any tier added to that gear is lost when it is transmuted.
It is a reasonable request. Some enhancement was added to the gear and it would be nice if the process of transmuting that gear managed to retain at least a part of that enhancement. That is not how it works, but it could make sense to make it work that way.
A request #1
Can we have a little more realistic depiction of the stat acquisition? The idea that you will buy stats from a vendor, while technically works, IS NOT how people get stats. So, a more realistic approach, with DOD stats, as well as explanation of how you run DOD and grabbed a bunch of gear that had the stats your liked would be more representative than "buy stats from vendor with mementos"
A request #2
This is a bit more complex, but what I would like to see when discussing clean transmuting is the handling of tiering while statting. It is a subject that I have not seen covered well in any guides.
Basically what I am talking about is this.
Let's say we want are making a lower level statted item. The steps will be:
1) Gear with stat A + Puri --> Mana Stone with stat A
2) Gear with stat B + Puri --> Mana Stone with stat B
3) Gear with stat C + Puri --> Mana Stone with stat C
4) Gear with stat D + Puri --> Mana Stone with stat D
5) Gear with stat E + Puri --> Mana Stone with stat E
6) Gear with no stat + Puri --> Mana Stone with no stat
7) Gear with stat F + Mana Stone with stat A + Mana Stone with stat B + Mana Stone with stat C --> Gear with stats A, B, C and F

Gear with stats A, B, C and F + Mana Stone with stat D + Mana Stone with stat E + Mana Stone with no stat --> Gear with stat A, B, C, D, E and F
Now, while this works, step 8 produces Tier 4 item. So, our final item might have all the stats, but it is only tier 4, and as such it is not taking full advantage of the stats and ghost stats.
What would happen if we wanted to produce a better item? We would need to tier it up. The process would then be:
1) Gear with stat A + Puri --> Mana Stone with stat A
2) Gear with stat B + Puri --> Mana Stone with stat B
3) Gear with stat C + Puri --> Mana Stone with stat C
4) Gear with stat D + Puri --> Mana Stone with stat D
5) Gear with stat E + Puri --> Mana Stone with stat E
6) Gear with no stat + Puri --> Mana Stone with no stat
7) Gear with no stat + Puri --> Mana Stone with no stat

Gear with no stat + Puri --> Mana Stone with no stat
9) Gear with no stat + Puri --> Mana Stone with no stat
10) Mana Stone with stat A + Mana Stone with stat B + Mana Stone with stat C --> Mana Stone Tier 5 with stat A, B, C
11) Mana Stone with stat D + Mana Stone with stat E + Mana Stone with no stat --> Mana Stone Tier 5 with stat D, E
12) Mana Stone with no stat + Mana Stone with no stat + Mana Stone with no stat --> Mana stone Tier 5 with no stat
13) Gear with stat F + Mana Stone Tier 5 with stat A, B, C + Mana Stone Tier 5 with stat D, E + Mana stone Tier 5 with no stat --> Gear Tier 5 with stat A, B, C, D, E, F.
In the process we had to use 9 puries instead of 6 and 13 charges instead of 8. We got our item to be with same stats as before, but one higher tier. The enhancements that come from extra tier would need to be weighted against the cost of 3 extra puries and 5 extra charges.
For lower level gear, that "tiering while statting" cost is probably not justified. For higher level gear it absolutely is. Most end-gamers are walking around with their gear at T6, and a few of them have pieces at T7.