I have LOTS of experinece with ZR sleds. I have a '98 and '02 ZR 600 EFI. I've rebuild this sled from top to bottom at least 3 times. If your sled runs good less than 30 MPH and dies if you give it full throttle, it's most likely the high speed stator coil. You can easily check it by measuring the impedance across the coil. It should be less than 50 ohms. Most likely it is open. I just had this problem last weekend. Anyting over ~6000 RPM and the sled would die. The ZR stator is a known problem. The coil insulation breaks down at high temperatures. I've replaced six stators in this sled over the last 3 years. You can get the stator rebuilt. Look in back of a SNOWTECH magaxine for "Stator Corp". They located are in Mass.
My experience with ZR electrical problems.
1) I've had the throttle safety switch fail twice. I finally disconnected it. Symptoms: Engine spuratically cuts out or dies. Engine monentarily feels like it is running on 1 cyclinder. This problem can drive you crazy. You may think that the engine is overheating, starving fuel, etc.
2) Eletrical grounds. The ZR has a bad grounding system. The engine is grounded to the frame near the exhaust sliencer via a wire from the engine. THe ECU is grounded to the steering bracket. Depending on the age of you sled and the amount of corssion due to dissimuliar metal (steel to aluminum), I've measure over 200 ohms resistance. I suggest that a 10ga wire be run from the ECU ground on the hadle bar to the ground point on the engine. This has cleared up many intermittent "ghost" problems.
3) '98, '99 cooling system. Because of the stator problem, I installed accurate digital temperature gauges on my '98 and '02 sleds. The ZR thermostat is set at 120 deg. The '98 runs consistantly 20 deg hotter than the '02. The '02 runs pretty steady at 123 deg in good snow. The '98 consistantly runs at 142 deg in good snow. I assume this is the main reason the '98 sled has gone thru so many stators. Note, when the trails are hard (regardless of temperature), both sleds can easily run at 180 -200 deg. This is hot. With just an idiot light, you really don't know how hot your sled is running until it comes on. If the trails are hard, I take the thermostat out. It can reduce temps by 30 deg or more. This can be easily done on the trail. Just remember to pull the rubber gasket off the themostat and place it back into the housing. When stopping for fuel, eats, etc. let motor run for 1 minute before shutdown. This allows the engine to cool a bit from running hard. Don't let engine idle for more than 3 minutes. Temps can easily get over 200 deg fast. Believe it or not it takes 2-3 miles running on good soft snow to cool a hot engine back down to operating temperatures after a normal fuel stop.