Clive,
Do you have schematics ? I'm going off a Pro Football schematic, which is a bit different, but the flipper coils have common 25V to all other coils. The fuse holder and also the "bounce" switch complete the circuit, so I'd be looking at the bounce switch next. It is a simple "tilt" switch on the bottom board. Use a jumper to short it out and play a few games.
Clean the flipper cabinet switches.
Check the "ball return control relay". This is "Q" on the PF schematic. This also completes the circuit for the flippers ONLY. This is the more likely issue.
As mentioned, transformers either work or fry !
