1~2 and 3. On CCDs, the amplifier is effectively in the corner of the sensor, but on CMOS, there is an amplifier built into each photosite, dispersed throughout the sensor. See here.
As mentioned in one thing I recently discovered, most DSLRs have an amplifier before the ADC. This amplifier is typically only a power of 2 amplifier (1 stop), so all partial ISO stops are digital. In addition, they tend to max at 800 or 1600 ISO and are all digital amplifications afterward. The following paragraphs assume a camera that maxes out its analog amplification at 1600:
Unfortunately, the 12 or 14 bit RAW files prevent you from doing what you describe. The digital amplification takes place before the RAW files are stored. There is a maximum value that can be stored, so when you shoot 4-stops overexposed, even though the ADC is not saturated, the RAW file will probably be clipped.
Yes, due to the analog amplification, RAW files at higher ISO do contain more detail. However, ISO 1600 and ISO 12800 should contain the same amount of shadow detail (unless there is some additional special processing OR the ADC has effectively more precision than whatever bit depth your RAW files are stored in).
Even though #3 is true above ISO 1600, an ISO 1600 RAW may contain more information about highlights because they can still be clipped through the digital amplification process. For this reason and perhaps others (battery life, effective buffer size), when shooting RAW, it may be beneficial to shoot ISO 1600 and simply post process later. Again, I have not tested this, and if the effective ADC bit-depth is higher than the RAW format's bit-depth, it will not be true.