Anything is a tool for Mechanical engineering. We have used wood for quick prototypes, stickgum and cigarette wrappers for insulators and shims, Silly Putty for shaping and molding, I bought some of my best tiny tools at Sewing Machine stores, Art supply stores and Fabric stores. You can even get a fair, inexpensive little CNC machine for quick and accurate R&D of insulators, shims or gaskets from Cricut. Look at the Marker 3.
Carbon paper and Dykem are common to analyze and refine interfering fit. Dykem comes in spray cans, Liquid with a brush in the lid markers and they have a spray removal solution. It sprays very thin if used properly.
This may be Your best bet to find out if the connectors are being poorly aligned, have too much pressure at specific points between the male and female connectors meaning the issue may be in manufacturing and not Your fault.
I suggested alignment pins for the opposite side of the connector and receiving holes would have to be drilled into the mating connector. These would have to be done by a very reliable machine shop.
In regards to; the existing pins may be to small allowing useless 'precision' due to the mating part rocking. Try a couple of descending thickness split shims to connect the terminals in stages, this will reduce some of the rocking. You may also try using an fixtured arbor press to provide an even insertion.