Hello Kate,
when you say rock do you mean literally solid rock or just stone or shale ? If it is solid rock then water won't be able to drain away ...even shale could be compact enough to stop drainage !! was there a lot of standing water on the area you now use for your beds? if so it could be that the water table is higher than the level of the soil. what I mean by that is : you are in an old quarry , so stone/rock has been removed altering the original ground level . Water could be seeping out of higher ground ,or even the ground below your beds? , effectively making a small shallow pond.
The gypsum would help the clay , but you still need to expose as much of the clay to it as possible ie dig and break up the clay as small as possible, then add the gypsum . Over time it changes the structure of the clay to a more friable type of soil . The manure should have broken down a bit by now , but I don't like to put it in too big to start with ...it does take longer to break down if left very large. To break down the manure will need plenty of worms to get to work on it first , are there any in the soil ? If it is very clay like then it will be fairly inert , so therefore not much in the way of microbes and the like . All needed to help break down organic material, and neither of which will survive long in waterlogged soil, as they need air to survive. If it is that waterlogged then you will have what boils down to an anaerobic compost heap. Thats the type that stinks, and tends to be slimey, aso like the stinkey stuff/mud at the bottom of ponds and lakes, which is basically rotting organic material such as leaves and the like.
You will have to work out if your veggie bed is acting as a sump for the surrounding area. If it is then you would have to lift it up above the water level , or drain the surrrounding area. If the clay has blue streaks in it then that is a good sign that it is waterlogged. If it is really wet then it may also smell like methane/sulphur or rotten eggs.
I would try and compost the manure on its own first . If it doesn't have much straw in it already then get some more and mix in with the manure , let it heat up then turn the heap , let it heat up again and then turn again . Do this 4 or 5 times , you will then have what looks and smells like peat , sort of , good compost . Hope some of that helps a bit anyway....good luck with it ...
cheers
Russ