Consider replacing the stand pipe with another pipe, perhaps a syphon system. Using the emergency spillway as the main drain can cause erosion issues. If the stumps are not d=going to interfere with maintenance on the dam, I am not sure that you will gain anything by pulling them. Time will tell if the deeper roots from the larger trees eventually rot and cause leaks, Not sure that adding clay around the exposed shoreline will do anything either. Might want to see how things look over a longer period of time to better gauge what issues you really have. If the stand pipe is rusted off, you might want to focus on that issue first. Do you know how much watershed you have? What is the pipe size? How many surface acres is the pond? Welcome to the forum! Lots of knowledgeable and friendly folks here.