If you can find those for 40-pin still, I would try padding them OR solder a frame + lid on the new motherboard or if you can find one of the RF shields that covered the whole left side of the motherboard (can't find a picture of it now, they are rare)... But yes the situation is tricky so I don't blame your solution really.
I know it's hard but ideally you would try to preserve this incredible chip, that is flawed like some old poststamp!
I totally relate to your love for the flaws. The MOS team was incredible at the time, true hackers at scale, and the flaws are documented history on their release early, release often process.
Yeah, that R1 deserves better. What would you use?