I used to be involved in the testing of very high end telecoms equipment, for EMC compliance, and with our "early" products it was always a fire fight at the end of the design cycle to try and make the product compliant, not always sucessfully.

Once the design engineers changed the strategy, to include EMC as part of the initial design, the problems either went away, or were of a much easier nature to solve.

Adding opto isolators will NOT make your kit immune to EMI, It will just isolate it galvanically.

All lines entering or leaving the kit should have suitable EMI filtering, and the enclosure should also offer EMI sheilding, and pay special attention to the power supply arrangement as this is often a good way for EMI to become coupled onto your kit. Also consider transient supression on the signal and power lines.

Also proper PCB design with properly designed power and signal planes, and supply decoupling will also reduce the suceptability to EMI. This can lead to the need for 6 or more layers, most 4 layer boards are actually poor for EMI.