The team reported that they had ____ the contract with tooth and comb before forwarding its recommendation.

The phrasal verb 'pored over' means to study or read something very carefully and attentively. When examining a contract minutely (the idiom 'with a fine tooth-comb' indicates thorough examination), the appropriate verb is 'pored over'. 'Poured over' is a common spelling mistake involving liquid, 'plied over' is not standard, and 'run over' means to quickly review or to hit with a vehicle. Hence option (a) is correct.