Thanks. Option 3 was my first thoughts. But I started thinking about the other 2 options, mainly because it removes the possibility of messing up the neck pocket. But the more I have thought about it, the more I have gone back to thinking option 3 is probably better.
Option 1 will be the least amount of work, if you use good technique. Basically rout some cavities in the areas that you want to patch, cut and fit some wood blocks to fit in the cavities. Epoxy them in, level the blocks with the top surface. Then recut your new cavities and holes. If the gaps around the wood plug blocks are fully filled with epoxy, they will be invisible under the paint.
Option 2 is a lot of work, unless you have a lot of specialty machines and fixtures to help you. After you fit and glue on the new top, you have to recut the neck cavity and the whole perimeter, in addition cutting the new pickup cavities. Option 2 is about the same amount of work as Option 3, making a whole new body from scratch.
Option 3 is the best choice if you also want to change the shape of the perimeter. You can glue in patch blocks to change the perimeter, but that's some work too.