Fender flare mod

I suspect if you check with AEV, you'll discover that the material for the flares is ABS and will be able to be bonded very well with your typical thick ABS glue for black plastic DRW pipe. (drain, waste, vent) You can test it with the scraps you cut out. (which I would save to glue over the gaps on the underside). ABS glues are solvent weld type products and work best when clamped with light pressure in this case so you don't starve the joint.

If it is ABS, then any of the typical polyester based body fillers will work well to cover and fill the seam. Scarf out the joint with something like 40-60 grit, apply filler, let cure and sand back to flush. Also means that simple sand clean and prep will work for most paints without a lot of attention paid to adhesion promoters although they won't hurt. This would be my choice for adding back a textured finish.
www.tcpglobal.com/SEM-39853_6.html?gclid=EAIaIQobChMIiKPrg6ma2gIViV5-Ch24YgEfEAQYAyABEgL4OfD_BwE#.WsF3h0xFx9A
 
Are yours molded around the filler neck bezel?
No they arent.
Post a pic of the rear driver side flare
That's the only stock pic I got. I already have the rears removed. 20171228_154200.jpg
 
No they arent.
That's the only stock pic I got. I already have the rears removed.View attachment 37643
Those are standard flares...Billiebob has an aftermarket kit called a highline, which moved the fenders and flares up about 3 inches. It allowed for much bigger tires with zero suspension lift. They are not produced anymore, but still in demand, as you can tell by the tears of @Chris and @Starrs