Yeah, the poly does make it look better. I am getting ready to sand and do my final coats tonight. I am not very good at the "light sanding with a fine grit" I have found that using steel wool is a horrible idea, bits of steel wool get everywhere. I am using a 320 grit sanding block for tonight to get out some dust nibs and other rough spots, I think that should work ok.
Yeah, this is a huge point. wood putty and wood glue should be avoided at all costs, even the stainable varieites don't take up stain like the rest of the wood, learned this the hard way. You can KIND of hide it with a careful application of gel stain, but its a lot of trouble. Next time I do this I am just going to tip the cab on its side when I stain it and do one side at a time, instead of trying to do all the sides vertically. It will quadruple the finishing time, but the results will be better.
I applied prestain conditioner, but the thing is, stained wood is never uniform in color, you will get variations of light and dark, and really, that is part of what makes stained wood so attractive, the variations of the natural wood. The problem is that a lot of the commercial wood products are dyed, where its all one uniform color against the grain. Its that type of finish that is just about impossible to achieve with a simple brush/rag and stain...