How does sunlight feel hot through glass? My confusion is this. I can shine a flashlight through a window at someone, and they don't feel any heat. Yet, sunlight shines through a window, we feel the heat. I want the scientific explanation of how one can feel heat from the sun through a window, but not from any other light source?  Is the sun emitting more than just photons?
The answer is this:
The sun is a major source of ultraviolet rays. Though the sun emits all of the different kinds of electromagnetic radiation, 99% of its rays are in the form of visible light, ultraviolet rays, and infrared rays (also known as heat).
I will assume that the infrared rays can pass through window glass without changing, and that is why we can feel heat from the sun through a window.
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 A: 
I want the scientific explanation of how one can feel heat from the sun through a window, but not from any other light source

You can feel the heat from other light sources; you need to get a better light source.
The sun delivers about 1400 watts of power to a square meter of the Earth at noon.  Get yourself 14 old-fashioned 100W light bulbs, wire them up into a one-square meter square, and turn it on.  It will get very hot, very quickly.  1400W is a lot of power.
By contrast your flashlight is delivering 3 to 10 watts per square meter, and a significant fraction of that wattage is lost to resistance in the bulb, so that's heating the body of the flashlight, not the target. If you had a thousand flashlights, things would be different. Maybe give that experiment a try! 
1000 flashlights is hard to come by, but 500W lights for illuminating construction sites are easy to come by, and they conveniently have a pane of glass in front of them, so all the light coming out of them is already going through glass. I was standing in front of one in a cold garage while stripping paint off of a bookcase this weekend, and I could definitely feel the heat from across the room.   Get ten of those and shine them on a thermometer across the room and see what happens!

I will assume that the infrared rays can pass through window glass without changing, and that is why we can feel heat from the sun through a window.

Not really.
As you note, the vast majority of the light energy from the sun that makes it to the surface is in the infrared, visible and ultraviolet spectrum. Ordinary glass is relatively opaque to infrared and ultraviolet, so when you get heated through glass, it's the visible light that is doing the heating.
This is why greenhouses work.  The visible light comes through the glass, is absorbed by the interior of the greenhouse, and then any emitted infrared light is unable to shine back out of the greenhouse, and remains trapped inside.

Is the sun emitting more than just photons?

The sun is emitting all kinds of interesting particles. 
It is emitting a truly staggering number of neutrinos; almost all matter is transparent to neutrinos so gazillions of them are passing through you right now and you'll never notice.
It's also emitting a variety of charged particles that do not make it to the surface of the Earth, thanks to our magnetic field, but you can see them interacting with the upper atmosphere in places where that magnetic field enters the Earth, namely, near the poles. Those are the northern and southern aurorae.
