I have no experience with JAL but AA flights normally credit to my account automatically within several days.

I wouldn't stress about it affecting your upgrade chances though. As far as opups go, I'm in the camp that believes gold status doesn't make that much difference. In the last three years s a Gold I can only think of one time I've been upgraded, even though many of my flights were apparently oversold.

You have the same chance for paid airport upgrades to F and UuA as any other status passenger.