DISCLAIMER: These notes are from the defunct k8 project which precedes SquirrelJME. The notes for SquirrelJME start on 2016/02/26! The k8 project was effectively a Java SE 8 operating system and as such all of the notes are in the context of that scope. That project is no longer my goal as SquirrelJME is the spiritual successor to it.
I believe the initialization with the method is finished. I allocate the exception register and all of the input arguments, I do not believe there is anything else to do.
Register entries need to be locked, because they could be allocated and then dumped onto the stack screwing with the order of everything. Also before a method call, a bunch of registers will need to be saved onto the stack so that the correct register and stack state is used when the method is called. Although that is optional. It would probably be best to do that in the native handler as it could save and restore register states as needed since it could vary on each call.
I should research how some other operating systems perform system calls.
Well it might not matter much.