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Why average force is based on ma*vfa and not ms*vfs?

Hi cm2hn, we could have used the space capsule final speed in part b), as you suggest, but that's taking a bit of a risk since we calculated the space capsule speed ourselves in part a), and we might have made an error in that calculation. Using the astronaut speed provided by the question is a safer approach, but outside of that, either speed is fine.

Why the speed of astronaut is negative? Would I get the same result if I use the capsule as the negative value?

The only thing that matters is that you're consistent with your coordinate system. This is to say that everything pointing in a particular direction needs the same sign (be it positive or negative doesn't matter, just that they're all the same), and things pointing in the opposite direction have the opposite sign. So, yes, you could make the capsule velocity negative, keeping in mind that this now means the force exerted on the capsule by the astronaut would also be negative in that coordinate system, since it would be directed to the right just the same as the now negative capsule velocity.