Welcome gklop, As a non professional pond owner here are my thoughts. You said you pond is 1/2 acre and is currently 3 or so ft. low. If that pond water level is the average low year to year, and if you plan for "full potential" includes fish, I would stock for the expected low water level. Simply because a 1/2 acre pond could potentially have 1/2 the water in it with just a few feet drop depending on pond contours etc. If you have supplemental water via well water or stream etc. then you can plan more aggressively as you probably already know.

For the stumps, simply because since they have been there since the 80's, I will assume the issue is ascetic or you want a swimming area that is stump free. Whatever the reason for removal it is always a chance to cause a leak. If you are going to remove them no matter what, if it were me as a novice, I would have several sacks of bentonite clay and a larger load of quality clay to patch the holes left by the stumps. In the hole apply a heavy layer of bentonite/soil mix and pack as a first layer 1" to 3" thick, then line the hole in 1" to 3" packed layers of regular clay for a total of at least three layers or until smooth if you want a smooth bottom. IMHO

Maybe you have quality clay on your property. Just as a side note stumps turned upside down are great fish attractors. Fish will stage off a tree trunk but they really like the root system because bait fish stage just off the roots, quite a bit.Hope you have a tractor to help.

Some of the pro's on the site will chime in here shortly, and they will most likely want to know some other info, as I would like to know as well. Questions like how deep is your pond, acre ft. of water, if you know. Do you have prior fishing records, what kind of fish are already stocked, do you test the water for PH,O2,alky,siski clarity, etc, aeration now or in your future, what are your specific goals.Most likely you will be asked to post Pic's, most of us are male, site oriented.Not to be a typical male, the women on our site like to look too.

Good luck and hope you reach your goal(s).

Life is more fun with a pole in your hand.