Well, step one would be to check your voltage. Make sure you're not getting any insane numbers at the flipper coils. If everything was really bad and fried, but the voltages are OK, I'd go for replacing the flipper section of your driver board. It's like two 6 pin chips, a common transistor, and some resistors.
As for the trigger not operating correctly, check your motor switches. There's two of them under the playfield. There's one that tells it when the shooter is in the home position, and one that tells it it's okay to fire. You may need to adjust that second one.