Regarding two, your father does not need an ITIN/SSN for your mother to file taxes as MFS. See here for more info. In particular it says:
Note that if she does choose MFS then she may more in taxes. In our case it was the difference of a few thousand, it may be more or less in your case, but for almost everyone MFJ will save money.
The IRS requirements for certified copies are very strict. My spouse had to go to the US Embassy to make a certified copy there. This would be done by the notarial division there. The process was fairly straightforward and cost $50. Only issue is the inconvenience of having to travel if the embassy is far away. Then your mother would send this certified copy, the application for ITIN, and your mother's tax returns to the IRS in one file. First they will process the ITIN application, then her tax return. It may take a very long time (think months) but it will get done. Also, since your father is not a permanent resident, your mother will have to also attach a brief letter stating that her spouse is not a resident for taxes purposes but wishes to be treated as such. Without this election she technically cannot file in the MFJ status. For more information see here. Also the W7 instructions are here. Note that full packet (return + W7 + certified copy of passport) must be sent to the ITIN office and not the usual address that returns are sent to (see the instructions for the full details).
Note, I think this reflects a misunderstanding in your original post, the ITIN application (W7) is filed together with the return, because he cannot apply for an ITIN without a reason (the reason in this case being he is married to an LPR who is filing a joint return).
Hope that helps!