We ended up replacing almost all the boards. The contractor wants to sand everything with three passes—60 grit, 80, then 150. He says that we should do this now to get rid of splinters and also level off variations in height. He says we should also seal and stain right afterwards with an oil-based stain to protect everything. 

I explained that we want to use a water-based stain, and our instructions are to let the wood weather for 3-6months first. He said we should still sand it smooth first (in 3 months). I said that anything higher than 60 or 80 grit wasn’t recommended because it blocks the pores from absorbing the stain. 

There are some parts that do need to be sanded, and he’s concerned we need to lower the screw depths and do a deep sanding.

Can someone please weigh in with specifics on what our recommended next steps should be for sanding and staining?

1. Replace planks
2. Sand*
3. Spray deck with water
4. Apply RAD cleaner with pump sprayer
5. Let sit for 15 mins.
6. Pressure wash at low pressure
7. Rinse. 
8. Apply RAD brightener with pump sprayer
9. Let sit for 10 mins.
10. Rinse for 20 mins.

*We have a large orbital floor buffing machine and were thinking of using a 60grit screen on this.

We would do this again (without the sanding) after the wood is weathered, and then add stain.
How does that sound?