I grew up with one of these things, lots of work but worth the trouble IMHO.
The scene in my head from your discription makes me believe that there's little hope of reviving the pond without a good cleaning, especially if you intend to put koi or any other type of fish in it.
Do you have an aquarium? The frogs could be captured and kept alive in a glass aquarium or set free somewhere else during the restoration. If you set them free, you'll find that after you restore the pond you'll attract new frogs among other things.
You should clean the entire pond out with and refill with clean water (If you have chlorinated water, you'll need to let the water sit for about a week before you try to put fish in it, check a pond supply store to see if they have a chemical for nuturalizing chlorine.
A pond needs to be a balanced ecosystem. Start with some aquatic plants. Lillies are really nice and relatively easy to grow, but you'll need some others to take care of the nitrogen and ammonia buildup from the fish. Once the plants are established you can begin to add fish. Only a few, they have a habit of breeding and becoming many. Frogs usually show up on their own, but you can go catch some for you own entertainment.
Clean the pond at least twice a year. Remove dead leaves and the muck that acculates on the bottom. We used to capture all the fish and frogs and put them the aquarium while we drained the pond and cleaned it. Never remove more than 70 ot 80% of the water when you clean it. There are bacteria in the water than the pond needs for balance.
There are lots of resourses on the web and in libraries for ornamental ponds. I'd reccomend you do a little research.