Made myself a chart of IDE to ATmega328 to Arduino layout pins
I tried to isolate the data heavy/sensitive pins with ground lines to avoid interference. I'm not too concerned about analog, but isolated Analog 4 for extra sensitive reads by putting it near 2 Analog ref lines
I was looking back at this idea of converting an ATmega328 into a pluggable module via an IDE 40 pin connector. It occurs to me that, most of the time, you would program a chip, drop it into a project box, and that's about it
Which means, it's really not necessary to have every analog and PWM pin connected at all times, just ones you're using (usually 5-6 at most in my case). And it's safer and simpler to have as few intrusions as possible into your enclosure for waterproofing too