My kitchen (1990) has red oak flooring that was stained honey/orange/brown. I’ve torn out carpet in an adjoining living room and hallway and now I am installing red oak flooring. My plan is to sand the finish off of the original floor, sand new floor and stain it all Special Walnut or something similar. I would like to stay away from any hints of yellow or honey. I’d appreciate any advice as to water/oil-based stain and poly. Also would love advice about drying time, # of coats, etc.

A light stain will not take as much work to look great. Since you would like a warm brown stain like special walnut you will need to spend more time sanding so no scratches show. I like to hand sand with 80 grit with some sharp scraper work to blend in the edges and field. A bastard mill file will keep the scraper sharp so you can make shavings will little effort. Scrape the corners before the final paper on the edger, then again after the fine paper and then hand sand.
After using an oil based stain, polish the floor with #2 steel wool to smooth any grain raise. One coat of stain is enough. Get any scratches out before the stain is dry, right after you see any. Shavings and dust will buff out with the steel wool when touching up as you stain a couple feet wide pass along the boards.
Two coats of oil based poly-urethane will give a pretty good wear layer. If you want to have an extra coat, then wait a week to hand sand with 120 and apply the third coat, otherwise the finish will be soft longer before it is cured.
DuraSeal is my preferred stain and finish. Go for satin poly.
Read the directions for best results.