Both water levels and rapid levels caused us to skip the gorge. There are a couple class V rapids, one named Wassons ends in a major sieve without really enough room to maneuver a raft - at low water levels you can line the rafts through safely, at the flows we had it would have been very unsafe. The kayakers on our trip did the inner gorge, the rafts portaged the entire section. High flows are generally Nov-March, outside those months I think the inner gorge would be possible. Aside from the inner gorge the rapids are similar to the Grand Canyon.
I'd definitely look up SierraRios: Kayak, Raft, and Protect Rivers in Mexico and Peru
if you're interested in running the Maranon, they have all the Beta and can help with logistics (or even easier join one of their scheduled trips - it's more like a private trip than a commercial trip but they help with logistics and have boats and gear you can use rather than dealing with boat transport).