Bill a couple more things that now come to mind:
1) 1400 rpm is a pretty low engine speed to test swapping injectors - try it again at 3000 rpm so engine has inertia.
2) Due to near idle conditions this could be a problem with Mode 2 adjustment and non-perfect match of PRI and SEC
 injectors.  The PRIs squirt directly into the housing; the SECs typically are much further away - the engine needs a moment to now get the fuel charge out of the intake/runners. My engine always stumbles for a split second - longer if engine or OAT are cold - I usually this check around 3000 rpm then go to controller B for coil checks.
3) Possibly there has been an incorrect setting in Mode 6: injector differential adjustment that has greater effect at low rpms Vs higher rpms.  If your injectors are all the same your Mode 6 compensation should be minimal.
Jeff

Have you tried all the previously-mentioned checks using controller B?

NO. TRYING THIS ON CONTROLLER B IS THE NEXT TEST.

I can’t think of anything else …  

DON’T STOP NOW YOU ARE ON A ROLL!!   :>)