Being water based stain you might be able to apply more water and blot some of the stain back out. It's worth a try at least. But the main problem you have is with the raised grain. Anytime you are going to use water based stain, you first have to wet down the whole project to raise the grain, let it dry. Then sand everything down. Then you can apply the water based stain.

Try a sample on some scrap wood. Stain just like you did on the kayak. Let it dry. See if you can re-activate the stain and blot it out with some water and a rag. After all this you will still need to sand down the raised grain and then re-stain, because I think that the whole blot and sand process will give you a fairly inconsistent stain job.

You can sand the raised grain and it will lighten it some. The eaiest way is to dilute your stain and apply a number of coats to slowly build up the color. You normally apply a really thinned out "wash coat" to raise the grain, sand and then build up the color. Glass and epoxy will darken it some and bring the grain out. Don't rush this part as you will not be able to undo a bad job unless you want to paint the deck.

 Wash coat and sanded

 Two thinned out coats