I cut mine out all the way around, then went and purchased a mudflap for an 18 wheeler. I just cut what i needed to close up the opening. I used a piece to go from outside inner to outside outer. I attached them with self tapping screws and washers (stainless steel).
Then i used a small piece of mudflap to close as much of a gap as possible, screwed a piece from the inner fender and tucked it inside the large piece of mudflap. And the same on the rear of the jeep, under the taillights, and tucked it inside the largr piece. I will get a little bit of water in there, but it runs out. Rubber won't rust, plus if i come down on a rock it will cushion somewhat. Plus, i have great clearance.
Oh! and if you want while you have that large opening, before you close it up, go and purchase those foam noodles that kids play with in the water, and cut them and stuff them up inside that large opening before you close it up. Helps with keeping too much water splash out of the fender (what little water gets in). And, helps with insulating and sound proofs a little also.
The only downfall i found is that, the rubber dry rots over time and needs replaced about every 2 years or as needed. Mine needs replaced before winter.