Should I replace motherboards?

before doing that try some resistors between the wire and the tab on the top of the can motors , low value resistors maybe 40- 70 ohms or so might slow the jack rabbit , resistors are pennies , you only need one per motor or 2 per engine , and you buy a few different values and try them till you get the speeds close , set up side by side test tracks and I guess make a lash up but run each loco on a different track once you get them all tracking the same distance  you have solved the problem , time consuming but easier and cheaper than what you are proposing .

Geep could be a candidate for the cruisem option.  You replace the odyssey board with the the ERR equivalent.  This may not fix everything as the GEEP may still have different gear ratios.

 Cruise Commanders don't support stall settings. I would replace the SD-35 with a Cruise "M" and the GP-30 with a Cruise "M" odyssey diesel. This will save you about seventy dollars and still have all the features. You will have nudge feature on both. But as Chuck said , you still might have a gearing problem.

Bill

Thanks for all the info and suggestions!