This seems like another one of those ideas/projects that requires working on a version of plane that will NOT be very good in service for 1 to 2 years so you can be ready with a tooled up production line
when the version of the engine you really want to use shows up.
It also requires a fair amount of jiggery-pokery to get it to work.
AS for availability of Hercules engines, details seem to be a bit sketchy but it took until Dec of 1941 to get the first 200 Short Stirlings.
The first Wellington Prototype with Hercules engines flew May 19th 1939 but the first production version didn't fly until the Jan of 1941 with the Hercules XI engine.
Photo of Halifax engine installation
View attachment 273700
Photo of the Zero
http://www.enginehistory.org/G&jJBrossett/RAFCosford/Nakajima Sakae 21 display.JPG
can't get it to transfer over.
It is not question of unbolting the Merlin and it's radiators and bolting on a Hercules "power egg" and bashing some sheet metal to fill the gaps. The Hercules has a higher carburetor than the Sakae and some other radial engines. It often used a remote drive to the accessories. Good for servicing the accessorizes, not so good for a short engine installation. The exhaust system is going to offer a lot less exhaust thrust than the Merlin. The cowl is not exactly low drag.
Everything can be 'fixed' with enough time and effort but the longer it takes the less need for it.
The Early Hercules doesn't offer anything the Melrin doesn't at the time and even a Hercules VI giving 1545hp at 15,500ft (Lumsden) is fighting higher weight and much higher drag than the Merlin.