IMO it sounds like you have two problems. A stuttering motor and poor economy. They may be related, but could also be two totally separate issues.
Firstly the transmission: Did you replace it with a new one or a 2nd hand unit? Are you sure the unit you fitted is from an RT and not from a GS or GSA? While the GS/GSA transmission will physically fit into the RT, the gear ratios are different. IIRC, the S, GS and GSA have a primary drive ratio of 1 : 1.823, while the R, ST, and RT have a primary ratio of 1 : 1.882. This could mess with your economy.
A telltale indication as to whether what you have installed is an RT transmission is whether it is painted or not. The RT casings are left unpainted, while the GS/GSA casings are painted/powder coated/whatever.
The stuttering motor: I would start with checking the stick coils individually. This is how I do it.
Replace all 4 plugs with new ones. (NGK DCPR8EKC)
Unplug the upper coils completely. Do not remove them. Just unplug the harness on each one.
Now start the motor. It should start and idle just fine. If it sounds like it is running on only 1 cylinder, then you have a bad lower stick coil. To determine which one is bad, unplug either one of the lower coils while the motor is still running. If there is no difference to the idle, you have unplugged the bad one. If the motor stalls, you have unplugged the good one. Bear in mind that you will only be able to rev the motor up to around 2800RPM with only the lower plugs connected.
Once you are happy that the motor is running well on only the lower plugs, switch off unplug them both. Now reconnect the upper coils and start the motor again. Once again, the motor should start and idle fine. If not, repeat the unplugging process as per the lower coils to determine which one is faulty. With the upper coils connected the motor should be able to rev as normal.
Finally, connect the GS911 and reset the adaptations.
If using the PC App, go to "Engine" > "Service Functions", the select "BMSK Adaptions" from the dropdown list on the right. Below that, select "Reset Adaptations" from the dropdown list, and then click on "Run Function".
The Web App is the same sequence, it just looks a little different.
Hope this helps.