I would say you have multiple problems,
Pop bumpers on system 1 s are only activated via pop bumper switches.
Flipper is activated by the side flipper switch.
Check side flipper switches for damage or broken wires.

Also double check you have the connectors on the right way round, at the board end.

Lights out gi or controlled
You may have a short circuit between the lamps and solenoid wiring

Donot power on til you double check all these.

Ok it looks like I had not insulated the lamp holder in one of the pop bumpers well enough and it has shorted against the bracket. I will tidy this up first give everything a thorough inspection and try again.

Thanks Riverina! :)