GhaleonEME

You would be better off downloading the full transcript from the IRS, you can use the return but you have to also provide copies of the W2's, previously that could be quicker for some but now you can just download & print your IRS tax transcripts so it is a no brainer.
For your 2013 income you can attach the letter from your employer along with some of your most recent pay slips and/or file your taxes so you can include the tax return + W2's.
You can just leave that section of the I-131 blank or put unknown.

1. Up until April 15th you can just supply the 2012 transcript
2. I131 & I765 have no fee when submitted as part of an I485 application, whether you file at the same time or later in the process. However you should file at the same time so the EAD can be issued quicker.
3. Yes, you should always file the I-131 as you never know what might happen in your wife's home country necessitating her going back

I just received the requested letter from my employer, and I am a little concerned that it does not explicitely state that my status is full time and permanent. What do you think?
To Whom it May Concern:
XXX was hired by XXX in September of 2012. He is a Systems Analyst for our firm. XXX is in good standing with the organization. His current annual base salary is XXX.
Please let me know if we can provide any additional information. You may reach me at email: XXX or call me at XXX
Sincerely,

XXX