If the suction cup lead is included in your resistance measurements, then a high voltage rectifier (several silicon junctions in series) are also included. Your ohm meter probably does not contain a high enough voltage source to forward bias this string of diodes to indicate approximate coil resistance. Add a couple 9 volt batteries connected together in series and use the milliamp meter to find out which low voltage winding is also connected to the high voltage output (positive) lead. You will need to connect the negative side of the battery to the the suction cup to forward bias the rectifier, since it is designed to produce a positive output voltage (and block it from going back into the coil).
Unfortunately for you, PMTs need a high negative voltage with respect to the near ground output. So you will either have to find a flyback that has a diode that can be reversed, or has the diode external to the flyback transformer (rare these days).