It currently takes 512 right-click actions, or about 100 seconds, to fully upgrade a metal crate with x64 upgrades. It'd be very helpful if you could apply an entire stack of upgrades at once, perhaps by shift-right-clicking.

You know you could have saved yourself the effort and combine them into a bigger upgrade.

Unless you're playing with SF4 in which case they have custom recipes and possibly disabled upgrade combining.

Yes, this is in SF4, I didn't know that you can normally combine them. I guess it's not really an issue then - normally you can combine them, and SF4 has auto-clickers.