Do your tanks have filters? Is one of them a canister filter? You could place the return of the canister filter into the grow bed, and have the grow bed drain into the tank. You still need to figure out a way to ebb+flow, but at least your water is being pumped to the right places.
(I'd also make sure I didn't accidentally drain all the water out of the tank into the grow-bed and onto the ground.)
Option #2: Take down one tank, remove filter, replace with pump, restart the cycle using your new aquaponic filter.