I also worry about the strength of the Subaru transmission. But I think it'll be fine as long as not too much as asked of it. The finished car will be almost half the weight of a stock WRX and the custom rear axles should be beefier than the stock WRX axles.
We'll see about gears. Either way, I'm putting hardened gears in mine, but I haven't decided which ratios to go with. The lighter weight might make the 5mt stock ratios actually preferable in an AutoX environment.
On the Plus side of things, it'll have dual wishbone front suspension, multilink rear, and coilovers standard. The finished car will be about the size of a Miata, but with a longer wheelbase, slightly wider track width, noticeably less weight, and potentially MUCH more power. This thing is going to handle like a dream and be scary quick.