Microwave ovens are probably the most dangerous of consumer appliances to service. Very high voltages (up to 5000 V) at potentially very high currents (AMPs) are present when operating - deadly combination. These dangers do not go away even when unplugged as there is an energy storage device - a high voltage capacitor - that can retain a dangerous charge for a long time. If you have the slightest doubts about your knowledge and abilities to deal with these hazards, replace the oven or have it professionally repaired.
Careless troubleshooting of a microwave oven can not only can fry you from high voltages at relatively high currents but can microwave irradiate you as well. When you remove the metal cover of the microwave oven you expose yourself to dangerous - potentially lethal - electrical connections. You may also be exposed to potentially harmful levels of microwave emissions if you run the oven with the cover off and there is damage or misalignment to the waveguide to the oven chamber.
There is a high voltage capacitor in the microwave generator. Always ensure that it is totally discharged before even thinking about touching or probing anything in the high voltage power circuits.
To prevent the possibility of extremely dangerous electric shock, unplug the oven from the AC outlet before removing the cover and do not plug it in to operate it with the cover off if at all possible. If you must probe live, remove the connections to the magnetron (see below) to prevent the inadvertent generation of microwaves except when this is absolutely needed during troubleshooting. Discharge the high voltage capacitor (with the oven unplugged) and then use clip leads to make any connections before you plug it in and apply power. Then after removing power and unplugging the oven discharge the HV capacitor once again.
WARNING: Experienced technicians have been electrocuted deader than a brick from even careful probing of the HV circuits of a powered microwave oven. Therefore, I highly recommend avoiding any probing of the HV circuits - nearly everything can be determined by inspection and component tests with the oven unplugged.
The microwave oven circuitry is especially hazardous because the return for the high voltage is the chassis - it is not isolated. In addition, the HV may exceed 5000 V peak with a continuous current rating of over .25 AMP at 50/60 Hz - the continuous power rating of the HV transformer may exceed 1,500 W with short term availability of much greater power. Always observe high voltage protocol.