First of all, I'm absolutely in love with this mod, thank you for making it!
If I understand it right, the green arrow on the chip sets the order of the I/Os when the chip is placed. However, once it is placed you can press R on it and the arrow rotates while the I/Os dont.
Since rotating the I/Os after the fact is probably needlessly complex, I propose just disabling the ability to rotate the chip after placement.
Additionally, it'd be great if the arrow could point towards pin 1; I've noticed it points to 3 on the small chip for instance.