So for anyone else following this thread, I finally got in touch with someone from EVA.
Their "official" response to this scenario is that I'd have to go through security and customs, then fetch my bags and check back in for my onward JAL flight. However, EVA sould "try to help" with the transfer as much as they could.
The rep I spoke to estimated that 2 hours would be a reasonable expectation for such a transfer.