No OBDII check engine codes? When it shuts off, does it immediately stop (electrical/ECU) or sputter to a stop (fuel)?

My bet would be that one or more connectors or grounds on your new engine harness has gone intermittent due to a loose connector, connector dirt or corrosion, loose or corroded ground.

I always first suspect any parts that were not factory-installed - putting complex modern cars together is very demanding, even for expert mechanics.

Your fuel pump may be going bad.

Here's a case where an inexpensive scanner would be useful to get an idea of what's happening here.

Stalling at stops can be caused by several reasons.

Air/fuel issues or ignition circuit issues.

You have to nail down which one it is to begin your troubleshooting.

These days, even cheap scanners can record live data and that would be helpful in your case. A lot of them can even graph it.

So, you could pick a day when you're running errands around town and you know you'll be in heavy traffic and you'll encounter a lot of stop lights.

Hook up the scanner and record live data of your A/F sensor.  If your scanner lets you, also record fuel trims at the same time. 

When your Subaru stalls see if the engine goes lean just before it stalls. Then you'd start considering throttle body, IAC valve, PCV valve or any general "unmetered air" issues or like @chucktobias says, maybe a fuel pressure issue. (your mechanic "cleaned the fuel hoses" so he also considered "fuel starvation" ((not sure why he thought that was necessary unless they found an obstructed fuel line and that shouldn't happen without another issue)).

Conversely, if the engine goes rich just before it stalls at a traffic light, then maybe a sticky EGR valve.

If those don't seem to be the issue then the next time, record the engine rpms.

One of the things the computer uses the Crank Sensor for is to determine engine rpms. 

So it might be helpful to record the engine rpms to see if the signal drops out just before the engine stalls.

You have a 2 wire Crankshaft Position Sensor.

It's a VRS (Variable Reluctance Sensor). It creates its own AC voltage instead of using a DC voltage reference/ground from the computer like a Hall Effect Sensor.

With a VRS sensor, the voltage signal to the computer is "weaker" at lower rpms than at higher rpms and if you had a failing crank sensor, or maybe an intermittent wiring/connector issue like @glen_stet proposed, this should show up by the RPM data dropping out just before the car stalls.

Here's a graphic which may be helpful to wrap your head around something happening like this.

The computer doesn't really care about the voltage level as long as it can see it.

It cares about the time between the voltage signals.

So maybe that's helpful to see how a problem here could cause an engine stall at a stoplight. (failing sensor or wiring where the computer can't read the voltage at low rpms)

Don't get me wrong, I'm not saying to replace the crank sensor, throttle body. IAC valve, PCV valve, and EGR valve.

Just sayin' that recording Live Data on a "stop and go day" on some of the engine control sensors may be really helpful (Not just the ones I mentioned).

If you want to try this and you aren't used to this stuff, I'd suggest buying one of those BlueDriver scanners that work with your phone.

First, because they're inexpensive and I've never seen this kind of customer support for novices. They make videos on how to do all this stuff. And second, there's plenty of youtubes from different people, without any automotive experience, showing how they use it.

For example, I did a youtube search for "BlueDriver record live data" and this video came up.

https://www.youtube.com/watch?v=nPWzzDckghc

Even if you don't do your own repairs, with an intermittent problem which (like all intermittent problems never happens when your mechanic is test driving your car), you can show him the live data from several sensors when the engine dies at a stoplight which can help him narrow this down