Shimming the bonnet can be counter-intuitive and adding or subtracting a shim at one of the four points affects the other three in ways that are not immediately apparent. Because the bonnet is so long and wide, any slight angle adjustment at one of the four points will be multiplied at the skuttle and tops of the inner sills. If you seek to correct a resulting misalignment you will introduce another variable and compound the problem.
May I suggest you undo everything you’ve done so far and do a clean start? I used four, small wooden blocks to support the bonnet to its correct gap and elevation against the skuttle and then fiddled with the hinge shims.