Landed hard on bottom on waverunner and felt pain in lower back. Felt fine shortly after. Headache several hours later. Brain/spinal damage likely?

Piledriver Injury. I would recommend an evaluation with at least a neurologist for the headache. Such injuries transmit high energy force up the spine, and often i see traumatic spinal fractures with this mechanism of injury. I'm uncertain if there can be a type of post-concussive headache, but it may be possible. If the back still hurts, seek out a spinal opinion.
Refer to Neuro/Spine. This is something that needs evaluation by a specialist. I will refer the question to our neuro and ortho spine doctors, but someone with such an injury should be seen at a local medical center.