any tips on cleaning out the cowl?

You guys got me thinking. I have had the front and rear glass seals replaced but still getting water inside. I took the heater box out and the air box to cowl seal was only half there. I have some left over trunk seal left that is going to be my new seal. The box and cowl area were clear of debris so I will do the same on the left side air box. Gonna be a full weekend job with the cookout interruption today. Will shoot back to post what I find on the other side.