The factory says to swap them around if there's no spark on one or more.
Try this:
1. DVA readings should always be taken with everything hooked up. 2. Check for broken wires and terminals, especially inside the plastic plug-in connectors. We recommend that you remove the pins from the connectors using the Rapair R97-6 pin removal tool and visually inspect them. 3. Check the flywheel for broken or loose magnets. 4. Disconnect the kill wires from the CD and connect a DC voltmeter between the kill wires and engine ground, turn the ignition switch on and off several times. If, at any time, you see voltage appearing on the meter, there is a problem in the harness or ignition switch. At NO TIME SHOULD YOU SEE BATTERY VOLTAGE ON A KILL CIRCUIT. 5. Visually inspect stator for burned or discolored areas. If found, replace the stator. If the areas are on the battery charge windings, it indicated a possible problem with the rectifier. IF NO FIRE ON ANY CYLINDER: 1. Disconnect the kill wire AT THE PACK. Check for broken or bare wires on the unit, stator and trigger. 2. Using the Fluke meter with the 511-9773 peak reading adapter, or CD-77 and 511-9770 piercing probes, measure DVA voltage of the stator between the output wire sets. With everything connected, readings should be approximately 180 volts or more. Resistance readings between the stator wire sets is from 680-800 ohms (CDI will read 300-400 ohms). 3. Disconnect the rectifier and retest. If the engine fires, replace the rectifier. NO FIRE OR INTERMITTENT ON ONE CYLINDER: 1. Check stator and trigger resistance, trigger wire sets read approximately 50 ohms between the wire sets (DVA 5V or more), stator reads 680-800 ohms (DVA 180V or more) from blue to yellow. 2. Disconnect kill wire from one pack. If the dead cylinder starts firing, the problem is likely the blocking diode in the other pack. NO FIRE ON TWO CYLINDERS: If two cylinders from the same CD unit will not fire, the problem is usually in the stator. Test per above. ENGINE WILL NOT KILL: Check kill circuit in the pack by using a jumper wire connected to the kill wire coming out of the pack and shorting it to ground. If this kills the pack, the kill circuit in the harness or on the boat is bad, possibly the ignition switch. COILS ONLY FIRE WITH THE SPARK PLUGS OUT: Check for dragging starter or low battery causing slow cranking speed. DVA test stator and trigger. HIGH SPEED MISS: 1. Using the Fluke meter with the 511-9773 peak reading adapter, (or CD-77) and 511-9770 piercing probes, DVA check stator voltage to each pack at high speed. If it exceeds 400 volts, replace the pack. 2. Disconnect the rectifier and retest. If the miss is gone replace the rectifier. 2 & 3 Cylinder Connections: Color Code Cross Reference Color Code Cross Reference FUNCTION OLD NEW FUNCTION OLD NEW Trigger Orange White/Orange Stripe Stator Blue Brown/Blue Stripe Trigger Green White/Yellow Stripe Stator Yellow Brown/Yellow Stripe Trigger Red White/Red Stripe Ignition Coil White Orange/Blue Trigger White/Green Stripe White/Green Stripe Stop (Kill) Circuit White (Brown) Black/Yellow Pack #1 (Firing #1 and #2 cylinders) Pack #2 (Firing #3 cylinder) Trigger: Orange (White/Orange) Pack: White/Orange Stripe Trigger: Orange (White/Orange) Pack: White/Orange Stripe Green (White/Yellow Stripe) White/Yellow Stripe Green (White/Yellow Stripe) White/Yellow Stripe Red (White/Red) White/Red stripe No Connection White/Red Stripe White/Green Stripe White/Green Stripe No Connection White/Green Stripe Stator: Yellow (Brown/Yellow Stripe) Pack: Brown/Yellow Stripe Stator: Yellow (Brown/Yellow Stripe) Pack: Brown/Yellow Stripe Blue (Brown/Blue Stripe) Pack: Brown/Blue Stripe Blue (must be connected to the Brown/Blue stripe on pack 1) Coil #1: White (Orange/Blue Stripe) Pack: Orange/Blue Stripe Coil #3: White (Orange/Blue Stripe) Pack: Orange/Blue Stripe Coil #2: White (Orange/Blue Stripe) Pack: Blue/Red stripe 4 Cylinder Connections: Pack #1 (Firing #1 and #2 cylinders) Pack #2 (Firing #3 and #4 cylinders) Trigger: Orange (White/Orange) Pack: White/Orange Stripe Trigger: Orange (White/Orange) Pack: White/Orange Stripe Green (White/Yellow Stripe) White/Yellow Stripe Green (White/Yellow Stripe) White/Yellow Stripe Red (White/Red) White/Red stripe Red (White/Red) White/Red Stripe White/Green Stripe White/Green Stripe White/Green Stripe White/Green Stripe Stator: Yellow (Brown/Yellow Stripe) Pack: Brown/Yellow Stripe Stator: Yellow (Brown/Yellow Stripe) Pack: Brown/Yellow Stripe Blue (Brown/Blue Stripe) Pack: Brown/Blue Stripe Blue (Brown/Blue Stripe) Pack: Brown/Blue Stripe Coil #1: White (Orange/Blue Stripe) Pack: Orange/Blue Stripe Coil #3: White (Orange/Blue Stripe) Pack: Orange/Blue Stripe Coil #2: White (Orange/Blue Stripe) Pack: Blue/Red stripe Coil #4: White (Orange/Blue Stripe) Pack: Blue/Red stripe NOTICE: The color codes listed above may appear on the packs, stators or triggers. S