Electrical: Can a neutral wire just be capped

Can't be done as described, you are short 1 wire between the two light fixtures. You need another wire between the two lights. You do have other options though, one being a "smart switch" which uses a signal instead of travelers. How far apart are the 3-ways?

This is what your circuit looks like now.

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Start by turning the power off at the breaker, and verify power is off using a non-contact voltage tester.

When you look at the side of the receptacles, you'll see a small tab between the screw terminals.

Using a pair of pliers, break the tab off of the ungrounded (hot) side of the receptacles (the brass screw terminals side).

So your circuit will now look like this.

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If you left it like this the top half of the first receptacle would work with the switch, but the bottom half and the second switch would never have power. Using a small bit of black wire and a twist-on wire connector, remove the red wire from the screw terminal and connect it to the black wire and the top screw terminal. So your circuit looks like this.

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With the circuit like this the top half of both receptacles will be controlled by the switch, but the bottom will never be powered. To make the bottom half of the receptacles work, you'll have to use a bit of black wire to connect constant power to the lower screw terminal of each receptacle. When you're done, your circuit will look like this.

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Finish up by remounting all devices, installing trim plates, and turning the circuit breaker back on. At this point the bottom half of the receptacles should always have power, and the top should be controlled by the switches.

_{If at any time during this project you feel uncomfortable, do not hesitate to contact a local licensed Electrician.}

_{I'm just a guy on the internet, not a licensed Electrician. Assumptions may have been made on the current wiring, based on your descriptions. Without being there, there is no way to be sure these assumptions are correct. Please proceed with caution, and at your own risk.}