Silk screen is 21/25 for top. 23 is needed to enable selection of devices. 27 could be included if you like but it isn't normal to include values. Which ones are actually used depends on what you choose to make the Gerbers. For example, you could use 21 but not 25 to show the outlines but not the component reference (for when there is no room for the reference). 51 is often used as an assembly aid on small surface mount devices.
I saw a video about putting ">NAME" in tNAME layer so it will follow the schematic. What does this mean, I don't even know what is the meaning of "NAME"? I saw the video he wrote the name of the component ( say LM741) in tVALUE layer, that confuses me. Which one give you the reference like U1, U2 etc.?
Solder mask is "Stop" as you have guessed - 29/30. Solder paste is "cream" - 31/32. Most of these are automatically created based on design rules. Design rules also set the oversize for the solder mask. They also set the minimum annulus for inner layer pads.
Quite a few PCB houses supply DRC files for Eagle which are worthwhile using.
What is this, I am not familiar with this.
I am not sure what you want with your last question. Drawing on layer 29 will create a hole in the solder mask (it is a negative layer). If you want some copper covered in solder mask then it must NOT be a pad as they automatically get a mask. Use a track, rectangle or polygon.
I found the problem. If you smash the component in the schematic, you cannot update the location of the NAME and VALUE. Smashing does not prohibit the changing of the line changes of the symbol.I have never seen that problem. Have you changed anything in the base name of the part that could make it not recognize it as the same one?
Do you know of any ULP that can keep some of the existing reference destinations on the schematic, but refloat the rest of it?