I think pretty much all modern Pentax DSLRs have an AF assist beam, but a) it needs to be enabled in the menu and b) it will still show up pretty rarely (and c) make sure your finger is not covering it
).
AF tests should be done in good light, daylight, not indoors. Tungsten and LED lights can confuse the AF, and the lack of light can make it impossible to lock focus.
But if the focus ring was stuck that indicates that there is another problem - the lens, not the camera. Can you inspect the focus ring and make sure its circular and not squished/damaged? It could be that during shipping the lens got squished or rattled.
When you take a photo, does the photo look equally sharp on all sides? Or is perhaps one half of the picture significantly blurrier?
If I were you I would do the following:
a) inspect the mechanics to the best of my abilities. See if the focus ring works consistently or if there is a resistance at any point. Same for zoom ring. Check if aperture blades work normally. Make sure the mount is not damaged. Inspect the lens barrel for any cracks or abnormalities.
b) Make sure the optics are consistent and produce good images at any zoom, aperture and focus setting. If this works well, a repair might be worth it. But if you need repair, still ask the seller to pay for it (as in, give you a "retroactive discount" or activate the shipping insurance). The photo must also be consistent - all corners should have similar quality, center should be even better than corners.
c) notify the seller of what is happening. Do this calmly, list the problems in a clear fashion, and ask what they think - and whether they have some return policy. Do this as soon as possible if you havent already. Do not accuse the seller of anything, merely ask for an explanation and help. They probably want this issue resolved, too.
d) the SD card should in no way affect the AF functions of the camera. The 16-45mm, as far as I know, does NOT have its own focus motor - it relies on the camera's motor. Make sure the AF screw (and other contacts on the mount) are clean and free of particles or grime. Just take a look and maybe wipe gently or use a rocket blower. But if it works with other lenses, then it should be fine.
Can the lens damage the camera's AF engine? Probably not, but I can't guarantee anything. I would not try to use the camera's AF with a lens that has a stuck/damaged focus mechanism. Maybe the camera is smart enough to know when to stop pushing the AF, but I wouldn't bet on it. It seems too risky to damage a fine K-5 camera body just because one lens is behaving oddly.
Oh, and one more thing. The 16-45mm has an outer and an inner barrel. It extends when you zoom, so make sure that the inner barrel is not bent, too..