It was a struggle
I ended up abandoning the plug bodies and using heat shrink on each wire, still using the molex pins, and covering each assembly with the shrink. I used tie wraps to secure the completed connections and I have 24 hours of flight logged and the connections are working well.
I tried and tried to get the pins to properly seat in the small plug but I just could not so I tried this method. I will continue to evaluate over time.
Arvada, CO BJC
RV12, #401, Flying 2013, N612PC
RV6, 1996-2010 sold