How to separate ground efficiently in a thyristor circuit controlled by sensitive microcontroller
The example you linked to in a comment is layed out far differently from yours.

Before I try to explain what I think is causing your problems (and what you can do about it,) I'm going to list some a assumptions I've made based on things gleaned from your questions and the linked source of the original circuit.  These things should have been in your question(s.)


You are generating about 200Vdc on board using a UC3843.
The 200Vdc are used to charge a capacitor (1.5uF)
The capacitor is discharged through an SCR, generating a high current spike to drive the ignition coil.
The high voltage for the spark is not actually generated on board - the ignition coil is probably the one originally used in the vehicle.




You have a problem with the discharge current.  As far as I can tell, the discharge current flows through the ground plane under and around your processor.

Given that the point of a capacitor discharge system is to drive a high current through the ignition coil, the discharge current will be pretty hefty.

That current can cause voltage differences across your ground plane, and induce currents in other traces.

These voltages and currents can cause your processor to do strange things.  

To top it off, you have many unconnected pins on your processor.  These can pick up the induced currents and voltages.

What you need to do is to keep the high discharge current away from your processor.

You should try the following:


Use separate ground planes under the processor and the CDI section.  These two are electrically connected, but only at a single point, and that far away from the high current areas.
The discharge path should be as short as possible, and it should not cross the path of anything sensitive.  Imagine a line from the CDI output, through the SCR, through the ground plane, and out to your ground wire.  No sensitive parts should be close to that line, and no sensitive traces should cross it or run parallel to it.
You need to connect all of those floating pins on your processor.  Tie the inputs to pull ups.  Any interrupts must also be pulled up.  Check the processor's datasheet to see what it recommends you do with unused pins.  
Check that you have adequate bypassing on all power supply pins for you processor.  The datasheet should tell you what to use.  Put the capacitors as close as possible to each pin, and use the shortest traces possible - and connect the ground side of each capacitor directly to the ground plane.


The layout of the original is rather higgledy-piggledy, but manages to keep all of the high current activity away from the processor.  It uses something like star grounding (accidentally, I'm sure) in a way that routes all the high current from the discharge around sensitive sections.

You have large ground planes that appear to be completely shared between the processor and high current sections.  Those let the high currents flow where ever they want to.  They will go (mostly) by the most direct route, but the discharge will cause really sharp edges that pretty much "broadcast" RF noise all across your board.