I figured it out. This is what I did:
1) Ingest a healthy dose of caffeine and reread post
2) Use Knit Surface to join all surfaces on the model. There were a few gaps:
3) Use Filled Surface to patch up that five sided headache. I made every constraint "curvature."
The ripple is due to to branching section having some high curvature in the cross section that was propagated to the surface. Smoothing the cross sectional sketch splines should reduce those surface ripples.