This is where speed matching comes in. I don't think the Bachmann decoders in these locos support CV's 5 and 6. You may want to replace them with ones that do. They should be the kind with an 8 pin connecter on one end.  Google speed match DCC locos for more info.  Sondtraxx and Digitrax both sell motor only decoders with the 8 pin connecter. Joe

It may not be obvious, but take note that the "B" unit actually is coupled "backwards" compared to the "A" unit.        Just curious what makes you say this?    Joe

I haven't tried it but a Kadee # 23 or E-Z Mate® Mark II Center Shank - Short  might work.   Joe
http://shop.bachmanntrains.com/index.php?main_page=product_info&cPath=258_273&products_id=4458
http://www.kadee.com/htmbord/page23.htm

Also what radius curves are you running these on? This will affect how close you can them to each other.

Make sure the 2 plugs between the tender and loco are in all the way. Are you running this on address 3? It's the default address from factory.    Joe

The GP7 and GP9 frames are the same. So yes you can switch shells.   Joe

LED is for the + and - side of the headlight LED, L is left side wheel pick up R  is right side wheel pickup,M1 andM2 are motor leads.  Joe

If it has a separate decoder with an 8 pin connecter on it you can make your own jumper. Buy one of these: http://www.modeltrainstuff.com/Train-Control-Systems-1255-CBU-8PIN-PLUG-CIRCUIT-B-p/tcs-1255.htm    you'll need to figure out which pins to connect.   Joe  

That should work fine for both loops. How many locos are you planning on running on both loops? Sound or non sound? I don't know the AMP rating of the Dynamis.   Joe

Yes. But the loops have to be wired together to the DCC command station/booster. What DCC system are you using?   Joe

Are you running it on a DC layout? If so this is normal as a DCC  sound decoder takes around 6V on DC before it will turn the motor. You're then left with about a 6V range for speed control. If you have a DCC system what is the system?   Joe

If I still have my AR-1 or MRC version, I may try and take it apart to see what it looks like inside the relay. If successful I will post photos.    Joe

I believe SCRAM is a layout design software.  Joe

  Maybe burn out isn't exactly whet happens. Even though DCC voltage is low, some systems put out as much as 10Amps. When the contacts in the relay move, there could be pitting of the contacts or a build up of metal on one side. If the build up gets high enough, the contacts could be welded together. Or the solenoid gets fried. I'm going off personal experience. I had 1 Digitrax and 1 MRC relay style AR's go bad.  My friend had 1 Digitrax  AR go bad as well.  Joe

Set CV3 to around 30 or so. This will cause the loco to get up to speed slowly. CV4 should  be 0 as this will cause the loco to stop almost instantly when the throttle is turn to 0. If the decoder has cv5 and cv6, set cv6 to 40 and cv5 to 70. This will limit the top speed of the loco. Even if the throttle is full speed, the loco will be moving at a reasonable speed. Experiment with the CV5 and CV6 settings to adjust the top and middle speed. I have a small switching layout and set my locos to run around 35 scale MPH at full throttle.  Joe

CV3 is acceleration, CV4 is deceleration. CV2 is start voltage. CV2 affects at what speed step the loco starts to move. CV3 is how long it takes the loco to get up to speed. IE: if you turn the speed nob to speed step 20 and CV3 is zero, the loco will accelerate rather fast. Adding a higher value will cause the loco to accelerate at a slower pace. The higher  the value, the longer it takes to get to speed. CV4 is the opposite: how long it takes a loco to slow down when the nob is turned to zero. This is a simple explanation as people use the speed nob differently. Some turn it slowly to get the loco moving, others crank it up fast.    Joe