So taking off just the first cover, I don't think it was taken apart. I was going to take it all apart but it looks like the nuts that hold on the gears have been crushed to hold them on. So if parts have been taken out, the transmission was installed by someone who knew what they were doing.
Someone is going to have to tell me if that looks like a stock fork because I haven't ripped into too many transmissions before and have nothing to compare it to.