I'd start with the Linux side.
The drivers in the Amithlon kernel have been modified to give more direct access from the Amiga side, so you'd want to extend that. Looking at the diffs makes them pretty obvious.
First, get 3D working on the Linux side without using X. Your best bet might be DirectFBGL. This might give better 2D as well, the drivers are much better now than they were back then, but you'll need to keep those old Amithlon patches working too.
Then you'd probably want to modify Wazp3D to use your 3D extensions instead of software rendering.
I haven't really looked at Warp3D, but I'd assume it's some modified subset of OpenGL. With any luck, you'd mostly end up with the calls being passed pretty much straight through to DirectFBGL.