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).