we had a terrible storm here last night and two of my cnc machines were on, one a mitsubishi mtc-10b has an alarm: Y03 AMP UNEQUIPPED, and the spindle drive has no led's on, but the axis drives light up, second a wasino lj-63m is in emergency stop and wont come out, there is no alarm message either, when i checked voltage on these machines it was good at the service box, the mitsubishi was good, but the wasino has 86 volts on one leg, is this a bad transformer??

It obviously looks like you got a hefty overvoltage spike, unfortunatly the Y03 is an amplifier fault that can be a few things but in this case hopefully is the power into the amplifier, check the three phase supply to the amps for a lost phase, it is possible it took out the amp, the problem with the Wasino, 85v is symptomatic of a lost fuse and you are reading the backfeed from the other two phases, check as much of the three phase supply as you can at the top and bottom of all power fuse carriers. If there is a difference between the top reading and bottom, you have lost a fuse and hopefully thats all it would be, also check the voltage right at the transformer, bypass any fusing.
Al.