Decrease in fuel economy

[RoyB]

Greetings all.  I have removed the initial posting and placed it in this section.
The trials and tribulations of replacing the transmission has taken me in some new and curious directions.
After getting everything back together, I found that the fuel line connections started to leak, so I replaced them with new fittings from Beemer Boneyard.  (Thanks Jughead from BMWMOA forum)  The engine runs better, but still stutters at full throttle.
I put some Sea Foam into the tank along with some injector cleaner and ran it for a few hundred miles yesterday.  I have had this bike for many years, and have always averaged just under 50 MPG overall.  On the trip yesterday, I dropped to 38 MPG.
Even when I get spirited in the backroads of the Blue Ridge mountains, I seldom get less that 45 MPG.
There is no misfiring, stuttering or hesitations.  There is the occasional stutter when cold starting but that always clears up.
Coils could cause this, as could O2 Sensors.  Remapping the Throttle Position Sensors (open and close the throttle 3 times with th engine off) could play into this as well.  Has anyone else experienced this before and have any thoughts on where to start?
I have a GS911 but am not completely familiar with all of the options.  This is for a 2006 R1200RT with 68,000 miles on it.  Thanks

Update:  Yesterday I did the Remapping of the Throttle Position Sensor by turning on the ignition, then slowly opening and closing the throttle 3 times.  This improved gas mileage up to 43 MPG, but there is still an issue.  I plan on connecting the GS911 to the bike in the next day or so.  Hoping someone can point me in the right direction as to which test or tests should be performed with the GS911 so I can get to the point and resolve this problem.  Thanks

[Jughead]

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.

[RoyB]

Thanks again for jumping in.  The replacement transmission was from another 2006 R1200RT and is not powder coated.
Here is a link to an earlier thread from the BMW Sport Touring Forum where I was prompted to replace rather than try to find someone to rebuild the existing trans. 

https://www.bmwsporttouring.com/topic/98818-transmission-noise/?tab=comments#comment-1070322

The process you outlined makes perfect sense.  I will run through the process later this week and reply with my findings.

[RoyB]

Overdue response to this issue.  The lead into the upper coil was not making a proper connection, therefore only the bottom coil and spark plug were firing.  Easy fix once the tupperware was removed.  I put in new plugs and tested the upper and lower coils by disconnecting the lower and starting the engine, then reconnecting the lower and disconnecting the upper and starting the engine.  I found the upper connector was not seated properly which caused the engine to run using only the lower coil.  Once the upper coil connector was cleaned up and reattached, everything is back to normal.  Back to just under 50 mpg and proper running.  Thanks for the feedback. 

[e7navy1999]

try cleaning your MAF sensor in the airbox.  Use MAF spray from any autoparts store

[Marilina]

Thanks again for jumping in.  The replacement transmission was from another 2006 R1200RT and is not powder coated.
Here is a link to an earlier thread from the BMW Sport Touring Forum where I was prompted to replace rather than try to find someone to rebuild the existing trans. 

https://www.bmwsporttouring.com/topic/98818-transmission-noise/?tab=comments#comment-1070322 run 3

The process you outlined makes perfect sense.  I will run through the process later this week and reply with my findings.

The top coil and spark plug weren't lighting because the lead leading into them wasn't establishing a good connection. Once the Tupperware was gone, the problem was quickly remedied. After installing the new spark plugs, I started the engine with the lower coil disconnected, then reconnected, and finally started the engine with both coils connected.

[Haibarafs23]

Thanks again for jumping in.  The replacement transmission was from another 2006 R1200RT and is not powder coated.
Here is a link to an earlier thread from the BMW Sport Touring Forum where I was prompted to replace rather than try to find someone to rebuild the existing trans. 

https://www.bmwsporttouring.com/topic/98818-transmission-noise/?tab=comments#comment-1070322 fnf

The process you outlined makes perfect sense.  I will run through the process later this week and reply with my findings.

Yes, the replacement would be a better choice

[WayneC]

Does remapping the Throttle Position Sensor by turning on the ignition, then slowly opening and closing the throttle 3 times, will it affect the durability and safety of the engine?
death run 3d

The process of " turning on the ignition, then slowly opening and closing the throttle 3 times" is one of the urban myths which wont die which persist on the 650GS models no matter how many times it is debunked & is claimed at different times to calibrate/reset TPS

TPS position is read when ignition is turned on & 0 position is set, max position is set when to a default when reset under diagnostics command & the value is increased when riding & throttle is opened more than the default, all easy to see when using diagnostics & real time logging

[e7navy1999]

GS911 does have a throttle remap feature.  I have no idea if it works?

[Ruan]

Does remapping the Throttle Position Sensor by turning on the ignition, then slowly opening and closing the throttle 3 times, will it affect the durability and safety of the engine?
death run 3d

This is just spam, I'm removing that from the thread.

Wayne's answer is relevant though :-)

Kind regards
Ruan