I don't know if this will help but here's my 2� worth.

A friend has a pond that's about 1-1/2 acres and is kind of like yours in that it's sort of two different ponds in one. The upper section is an old old pond that is fairly shallow and weedy. A few years back they decided they wanted a bigger pond and built a large dam below the small one and dug out the area between the two dams to make a wide deep hole. The new water level is almost exactly the height of the old dam leaving a long island in the middle of the pond that is the old dam. Then when the lower section filled up they brought in a large backhoe (i think) and dug out 5-6 foot deep channels in the old dam along each shoreline to allow the aquatic life to move between the two sections. It's an awesome pond now that I really like to fish.

Because you have this barrier in the middle of your pond I wonder if you can use it to your advantage. My suggestion is that you look into pumping dry half the pond. Then have a more competent bulldozer operator fix up that part the way you want. Then let that half fill and pump the other half dry. Then bulldoze that part the way you want. Then have sombody cut some channels along the shorlines in that dam that's in the middle of the pond.

You could even get creative and have them build up the middle dam so that it could become an island year-round and maybe build a bridge from one or both shores out to that island which would give you easy shore fishing access to every surface inch of the pond. Another nice thing about doing it this way is that when you drain down half the pond you could capture any decent fish you expose and move them to the full half so you wouldn't be starting completely from scratch as far as your fish populations are concerned.

It might be quite a bit of work to do it this way but I think it would be really cool. That's my 2� worth.