Are you using only the internal pullups? A stronger pullup like 4k7 or 1k will overpower a lot of interference.Always try to route power wires in separate conduits or separate shielded bundles. Also consider any 12v devices may have significant inductive spikes that radiate interference.
How should i shield the bundles?
Why not mount your Arduinos close to their respective I/O circuits then use a serial connection between the boards to carry the data between them - simplifying and reducing your wiring.