For at least a little while you best bet will be a infrared camera to observe them from a distance. While they may work hard to mimic the characteristics you can see, they may not have tried to mimic thermal emmittance patterns yet. There are several reasons you probably already have one readily available.
SimularlySimilarly, their density is likely to have changed as silicon has heavier nuclei than carbon. One could place a scale in thoroughfares or require them to step on it before meeting with you.
An Xray would likely work if you can convince them to walk in front of a source. I would not leave one out to give all your crew cancer needlessly. Us Use it to screen those entering from outside. The benefit here is you can screen their internal structure.
As I do not know exactly what molecules/polymers/etc they are made out of, however, I cannot predict how these properties would change. I can only know that they likely would have.
An IR spectrometer would work well if their skin is still made of a silicone matrix or their blood is still artificial. But that would only help when the start finding a way to mimic your blood. As you need a reliable sample which means you need to take it. The main thing there is to not let any of them know how you are testing them... kill them if the test is positive. If you could build a portable, long range, broad spectrum spectrometer you would tax their mimicingmimicking abilities to their extreme.
Passcodes work well unless they can extract them from your wounded/dead/tortured comradscomrades.
I have one more risky suggestion for you friend. Microwaves ovens work well and hurt like hell because the molecules resonate with liquid water at 10 GHz while they run at 2.45GHz. Ammonia resonates at roughly 24 GHz and there is an ISM regulated frequency at roughly 24GHz. Aim it at a pet rat focused at him but at a low intensity. Point it at your Silisilici conarts and see how they react... I deal with complex Silicon materials all they time that are annoying transparent to microwaves. If their already pressurized and cooled blood boils begins to heat up however... The issue is whether you can find an intensity low enough people will barely notice be hurt but shifters will show perceivable damage. We have no ammonia in our bodies but there are alota lot of compounds which would resonate at different frequencies.